DIY BIO 4 Beginners

Synthetic cell breakthrough - Craig Venter creates a synthetic cell by assembling a chromosome with over 1 million base pairs

2010-05-23T12:18:00.003-04:00

Watch his interview with Gaurdian.co.uk here: http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-genome

Special thanks to Lianchao Han on the DIYbio mailing list for finding this great link.

Synthetic Biology Debate at Edinburgh Science Festival 2010

2010-05-18T08:33:00.003-04:00

Distinguished Cox Lecture with Dr. Jay Keasling from University of California Berkeley - Fall 2009

2010-03-25T14:25:00.004-04:00

Professor Jay Keasling of the University of California at Berkeley presents "Synthetic Biology for Synthetic Chemistry: From Bugs to Drugs & Fuel" at Washington University in St. Louis on October 30, 2009.

Part 1 of 5

Part 2 of 5

Part 3 of 5

Part 4 of 5

Part 5 of 5

BioBrick-A-Bot Project by University of Washington - iGEM 2009 Presentation @ MIT

2010-03-25T14:16:00.005-04:00

BioBrick-A-Bot Model C V 1.1 in action.

IGEM Presentation Part 1:

IGEM Presentation Part 2:

University of Washington Software Team. BioBrick-A-Bot Project to be presented at MIT from Oct 30- Nov 2 during
iGEM (Intl Genetically Engineered Machine) 2009
-------------
BioBrick-A-Bot is made up of an ALPHA Module and a PHI Module mounted on a BETA Frame.

BETA Frame: BioBrick Environmental Test Apparatus

ALPHA Module: Automated Lego Pipette Head Assembly
- Motor 1, Motor 2, Motor 3 used to position the pipette head accurately to any wells on the 96-well plate.

PHI Module
Pneumatic Handling Interface
- Motor 1 connected to a piston, either Aspirate or Dispense Fluid
- Motor 2 connected to 2 compression pumps, emit air jet to Clean Fluid
- Motor 3 controls a 3-way switch which selects one of 3 actions: Aspirate / Dispense, Nothing or Clean

Master Slave Synchronization
- Master Device : ALPHA Module
- Slave Device : PHI Module
- synchronization is programmtically controlled via bluetooth wireless technology

Andrew Hessel Talks About Synthetic Biology

2010-03-25T14:09:00.004-04:00

Andrew Hessel on the Future of Synthetic Biology

Andrew Hessel - Introduction to Synthetic Biology

Andrew Hessel - DIY Bio tookits

Andrew Hassel on Darwin and future labs

Andrew Hessel: Synthetic biology is the next IT industry

Andrew Hessel on DNA

Andrew Hessel discusses writing DNA

Andrew Hessel - Biology = computing

What Synthetic Biology Can Do For You - TEDxTerryTalks - Eric Ma - 10/03/09

2010-03-25T14:05:00.002-04:00

Links: http://www.ubcigem.com/ | http://terry.ubc.ca/tedxterrytalks.
Filmed by Craig Ross at TEDx Terry talks 2009 (October 3rd, 2009). Video edited by David Ng.

Beautiful blog: Synbiosoup - Research scrapbook for a project on Synthetic Biology Project at RCA Design Interactions by Gerrit Kaiser

2010-03-25T13:49:00.001-04:00

1 Min Video: Xiling Shen, at Cornell, uses engineering to tackle complex biological problems

2010-03-25T13:45:00.002-04:00

Synthetic Biology and the Corn Crop - a trip to the University of Illinois

2010-03-25T13:41:00.003-04:00

Podcast: James Collins - Engineering Life: The Past and Future of Synthetic Biology

2010-03-25T13:40:00.002-04:00

via: http://www.microbeworld.org/index.php?option=com_content&view=article&id=604:mts45-james-collins-engineering-life-the-past-and-future-of-synthetic-biology&catid=37:meet-the-scientist&Itemid=155

"In this podcast, I talk to James Collins, an investigator at the Howard Hughes Medical Institute and a professor at Boston University. Ten years ago Collins helped launch a new kind of science called synthetic biology. I talked to Collins about the achievements of synthetic biology over the past decade, such as engineering E. coli that can count, and about the future of synthetic biology--from using bacteria to make fuel to reprogramming the bacteria in our guts to improve our health."

Download: mp3 (37.5 min | 34 megs)

Joshua Leonard and Michael Jewett explain Synthetic Biology

2010-03-25T13:33:00.002-04:00

An overview of the emerging field of synthetic biology by Professors Joshua Leonard and Michael Jewett at Northwestern University's McCormick School of Engineering and Applied Science.

Science Daily Article: Biotech, Nanotech and Synthetic Biology Roles in Future Food Supply Explored

2010-03-25T13:27:00.001-04:00

Quoted from: http://www.sciencedaily.com/releases/2010/02/100221143238.htm
ScienceDaily (Feb. 25, 2010) — Some say the world's population will swell to 9 billion people by 2030 and that will present significant challenges for agriculture to provide enough food to meet demand, says University of Idaho animal scientist Rod Hill.

Hill and Larry Branen, a University of Idaho food scientist, organized a symposium during the American Association for the Advancement of Science annual meeting February 17 to explore ways biotechnology could provide healthy and plentiful animal-based foods to meet future demands.

Synthetic biology, nanotechnology, genetic engineering and other applications of biotechnology -- and the public's role in determining their acceptable uses -- were all addressed by panelists during the session. The goal for the session, which was part of the nation's largest general science meeting held annually, was to encourage a dialogue among scientists and the public, said Hill, a Moscow-based molecular physiologist who studies muscle growth in cattle.
"There will be a significant challenge for agriculture and the science that will be required to provide a healthy, nutritious and adequate food supply in coming decades for a rapidly growing population," Hill said. A key question, he said, is whether the Earth can continue to provide enough food without technological support. The history of civilization and agriculture during the last 10,000 years suggests otherwise.

"Unaided food production is an unattainable ideal -- current society is irrevocably grounded in the technological interventions underpinning the agricultural revolution that now strives to feed the world," Hill said. Branen serves as the university's Coeur d'Alene-based associate vice president for northern Idaho. He also remains active as a researcher working with nanotechnology in a variety of ways, including uses as biological sensors to detect disease or spoilage. Nanoparticles may be used to target certain genes and thus play a role in genetic engineering of food animals. Branen said, "There's also no question that nanomaterials may help increase the shelf stability of food products and assure their safety."

Other panelists include University of Missouri Prof. Kevin Wells who believes genetically modified animals will have a future place on humanity's tables, just as genetically modified plants do now. Panelist Hongda Chen serves as the U.S. Department of Agriculture's national program leader for bioprocessing engineering and nanotechnology. He will explore how scientific methods like nanotechnology may be applied to help meet the world's growing demand for safe and healthy food.

Synthetic biology, the use of novel methods to create genes or chromosomes, will be explored by panelist Michele Garfinkel, a policy analyst for the J. Craig Venter Institute, which pioneered the sequencing of the human genome. The public's acceptance or rejection of new technologies that could determine future food supplies will be the domain of Susanna Priest, a professor at the University of Nevada Las Vegas. A communications researcher, she has argued that public debate is essential to public attitudes toward such technologies. "I think that's essential," he said. "We've seen lots of technologies where we didn't get adoption because we didn't get consumer acceptance and understanding. Irradiation of food has been possible for over 50 years but we still haven't gotten to general use because there is still a fear and lack of understanding of it." Branen added, "To me everything we're doing today requires an extensive discussion and an interdisciplinary approach. We can't just focus on the technology but must look at the social and political aspects of the technology as well."

Open-Source Lab Promises Free DNA Parts for Bioengineers

2010-03-25T13:24:00.001-04:00

Quoted From: http://www.popsci.com/technology/article/2010-01/open-source-lab-promises-free-dna-parts-bioengineers

BIOFAB Drew Endy and Adam Arkin, director and co-director, respectively, of BIOFAB, at its temporary headquarters in the Emeryville labs of the Joint BioEnergy Institute. Margot Hartford

By Jeremy HsuPosted 01.25.2010 at 11:15 am - Poor Dr. Frankenstein had to steal corpses for his mad experiments, but modern-day bioengineers need not resort to such dubious methods for raw materials. The new Biofab laboratory plans to churn out thousands of free standard DNA parts that academic and private biotech labs can use to create new designer microbes that can make everything from new drugs to fuel.

This could give a significant boost for research efforts, considering that a single designer microbe may cost years and tens of millions of dollars. One University of California-Berkeley effort to engineer microbes that could synthesize an anti-malarial drug took a decade and $25 million to reach small-scale production.

Scientists from Stanford University and UC Berkeley have focused on identifying the thousands of molecules and processes so that they can mix and match DNA parts in the Biofab lab. Their funding comes from the U.S. National Science Foundation, as well as the Lawrence Berkeley National Laboratory and the BioBricks Foundation.

Open source as an engine for innovation has caught fire recently. Pharmaceutical giant GlaxoSmithKline has offered up thousands of chemical compounds from its database in hopes of someone finding a cure for the mosquito-borne disease malaria.

The Pentagon's mad science lab DARPA has also pushed for a similar business revolution along the lines of the semiconductor industry, where certain firms focus on innovation and leave the tedious manufacturing to semiconductor foundries. But in this case, Biofab would provide the raw building blocks that allow synthetic biologists to more quickly realize their dreamt-up creations.

Regenerating bodies

2010-03-25T13:19:00.000-04:00

Japanese Create Fluorescent Mario from Genetically Engineered Bacteria

2010-03-25T13:14:00.004-04:00

Quoted from: http://www.popsci.com/science/article/2009-12/japanese-create-fluorescent-mario-genetically-engineered-bacteria

Team Osaka's nanobiology lab created a petri-dish image of everyone's favorite Nintendo game character. By Jeremy Hsu - Seizure Mario Running seizure Mario!

Nintendo's Mario has taught us science and even encouraged the development of better artificial intelligence. So it's only appropriate that Japanese researchers paid homage to everyone's favorite video game character, by recreating his likeness in a petri dish with genetically engineered glow-in-the-dark bacteria. Warning: we reveal a seizure-inducing Mario animation after the story jump.

Team Osaka submitted their Mario likeness to the 2009 international Genetically Engineered Machine competition (iGEM). They combined standard DNA sequences known as BioBricks with their own special DNA snips to create franken-bacteria that express fluorescent proteins and carotenoid pigments.

You can gawk at this and other fine petri dish masterworks at this New Scientist gallery.

[via New Scientist]

Popular Science's DIY Bio Article

2010-03-25T13:10:00.003-04:00

Synthesizing New Life A City College of San Francisco team plans to make their mark at MIT's iGEM conference Douglas Adesko/NYTimes

Quoted from: http://www.popsci.com/technology/article/2010-02/future-biology-lies-designer-organisms

The Wild World of DIY Synthetic Biology: Get your designer life forms here! By Jeremy HsuPosted 02.12.2010 at 4:55 pm

"A new generation of scientists hope to become genome hackers who redesign organisms to become living tools, capable of creating diesel fuel or producing anti-malarial drugs. That synthetic biology revolution has led to a can-do spirit of innovation that has fueled MIT's International Genetically Engineered Machine Competition, known as iGEM for short. The New York Times has traced the route to iGEM by following a community-college team from the City College of San Francisco, as the group tries to build a bacteria-based battery powered entirely by the sun for iGEM. It's a great overview of one of the more exciting scientific fields today.

Genetic engineering has traditionally focused on swapping out single genes at a time. But synthetic biology represents something much wilder and more radical. Rather than cut-and-paste, synthetic biologists hope to create entirely new genetic code assembled from an open-source repository of snippets of working genes called "BioBricks." Assembling them like legos, the new sets of custom genetic code can then be re-inserted into bacteria or other organisms, modifying their fundamental behaviors and life cycles. This opens the door for scientists to engineer entirely new living organisms.

This redesign approach need not only take place in large private or government labs, as iGEM's student participation shows. Another example comes from DIYbio NYC, a group founded by NYU students that aims to make synthetic biology accessible to "citizen scientists, amateur biologists, and DIY biological engineers."

Synthetic biologists of all stripes already have a large set of genetic parts to work with. MIT has assembled an open-source library, called the Registry of Standard Biological Parts, that holds more than 5,000 BioBricks. iGEM teams have contributed the BioBricks from their projects, but they can also make use of the library for future work.

Technology, Jeremy Hsu, bioengineering, dna, genes, genomes, iGEM, MIT, synthetic biologists, synthetic biologyScientists from Stanford University and the University of California-Berkeley have also launched their own open-source genetic lab called Biofab. They hope to identify thousands of molecules and processes that would allow them to efficiently assemble DNA parts in the lab, which would then become available for free to any would-be visionaries.

There's hardly any limit to the early ambitions of synthetic biologists. Even the Pentagon's mad scientists at DARPA have expressed the wish to immortal living organisms with genetically encoded kill-switches. But iGEM teams seem intent on more practical or at least achievable goals for now, including a seizure-inducing fluorescent Mario based on glow-in-the-dark bacteria."

Louis Matzel at Rutgers University Improves the Working Memory of Mice

2010-03-25T13:04:00.006-04:00

Mice trained to improve their working memory become more intelligent, suggesting that similar improvements in working memory might help human beings enhance their brain power, according to research published today in Current Biology by researchers at Rutgers, The State University of New Jersey.
See the full article here: http://www.physorg.com/news188739131.html

Maryland's DIY BIO Group's: Wonderful List of Learning Links

2010-03-25T12:43:00.003-04:00

Wow, here is a great list of links from Maryland's DIY BIO group! Thanks! I posted some of them here, visit their website for more.

Quoted from: http://www.genoblasts.com/6.html

Some basic links about Synthetic Biology, Protocols, Regulatory Agencies

Fora TV Presents Drew Endy and Jim Thomas Debate Synthetic Biology: http://fora.tv/2008/11/17/Drew_Endy_and_Jim_Thomas_Debate_Synthetic_Biology
ArsSynthetic - Forum on SynBio: http://ars-synthetica.net/
Synthetic Biology Research Center: http://www.synberc.org/
GenoCad OpenSource Synbio Design Software from VBI: http://www.genocad.org/
Synthetic Biology Movement: http://syntheticbiology.org/
Introduction to Synthetic Biology: Andrew Hessel - You Tube (57:12): Introduction to Synthetic Biology
OpenWetWare - iGEM Associated Open Source Database: http://openwetware.org/wiki/Main_Page
National Center for Biotechnology Information: http://www.ncbi.nlm.nih.gov/
National Science Foundation: http://www.nsf.gov/index.jsp
Microbial Communications: http://www.clicker.com/web/microbeworld-video/Tiny-Conspiracies-332035.html
Synthetic Bio Equipment: http://www.synbio.org.uk/hardware/diy-lab-equipment.html
Molecular Station (Bioinformatics/Protocols): http://www.molecularstation.com/
NATURE - Methods and Protocols: http://www.nature.com/protometh/index.html
Focus In BioTech (WebCast): http://www.twit.tv/FIB

Legal Issues and Intellectual Property Resources

BIOTECHNOLOGY & GENETICS LAW: http://www.megalaw.com/top/biotech.php

DIY- Bio

MIT on DIY: http://mitworld.mit.edu/video/646
do-it-yourself biology: http://diybio.org/
H+ magazine with related articles: http://hplusmagazine.com/digitaledition/2009-winter/
DIY hardware on the web: http://www.hplusmagazine.com/articles/toys-tools/hackerspace-your-garage-downloading-diy-hardware-over-web
Frequently asked questions about DIYbio: http://openwetware.org/wiki/DIYbio/FAQ
Pre-requisites to success: http://88proof.com/synthetic_biology/blog/archives/174

Local DIY Community Spaces

Harford Space: http://harfordhackerspace.org/
The Node - Baltimore City Space: http://baltimorenode.org/
MAKE Community: http://makezine.com/
Frederick County Biotech Community: http://fredcobio.wordpress.com/
HacDC - The Capital City Space: http://hacdc.org/

DIY-Bio Projects & Kits

Counter Top DNA - Thermocycler: http://makezine.com/07/fingerprinting/
Project: SmartLab: http://projectsmartlab.org/
OpenSource InkJet Nucleotide Synthesizer/MicroArray: http://genomebiology.com/2004/5/8/R58/

For More visit Maryland DIY Bios Website: http://www.genoblasts.com/6.html

The Story of Taiwan's Tzu Chi University's IGEM Team

2010-03-25T11:39:00.000-04:00

Their project Midnight Apollo aims to reengineers GFP to become bright enough to be a viable light source.

Chris Seidel's 2008 talk at The Last HOPE - A GREAT VIDEO ABOUT THE BIOLOGY FIELD AND WHERE ITS GOING

2009-11-04T19:44:00.005-05:00

Special thanks to Mac Cowell for posting links to these videos on the DIY Bio mailing list.
One important note that I have mentioned before. The use of biohacking in the biology community simply refers to working with DNA. The word hack has been given a bad rap by the internet era, but this in no way refers to any malicious activity. Hack in this sense simply refers to genetic engineering.

Understanding Cultured Meat (also called in vitro meat)

2009-11-02T09:39:00.004-05:00

Cultured meat is a hot topic that everyone should start learning about. Essentially most of the products we eat are just a collection of cells that have been programed to work together in a certain way. That means that animal meat can be programed up from single cells and will be made of the exact same ingredients as traditional meat. But, by producing meat in clean controlled environments the product would no longer carry the environmental, ethical, and health concerns it faces today.

Here is a quick top line summary of those concerns:

Environmental: Meat production is a major cause of green house gas - more than transportation and is inefficient to produce as much animal feed is wasted. Current methods are not sustainable.
Ethical concerns: Factory farming and other forms of animal suffering. Anyone who has paid attention to the recent investigations into the food industry can see just how immoral the industry has become.
Health: Numerous illnesses, diseases. and health concerns arise from animal husbandry and packing animals close together. Avian flu, swine flu, mass antibiotic use leading to antibiotic immunity, and bacterially infected meats are just some examples.

We love you Cynthia Kenyon! A new video! (July 10th 2009)

2009-10-28T01:12:00.003-04:00

Thank you, thank you, thank you for all your hard work Cynthia! So many diseases are caused by aging. Keeping people younger longer makes our society healthier, more experienced, and wiser. Oh this is so exciting!

Professor Cynthia Kenyon (University of California, San Francisco, USA)
Summary: Scientists have long thought that aging just happens. Yet because of their genes, different species have different lifespans. From the roundworm C. elegans, we now know that aging is regulated, by specific genes. These genes also influence life span in mammals, including humans. This system, and its evolution, will be discussed.

Drew Endy Wired Magazine Video (posted on Wired on 10/26/09)

2009-10-28T00:59:00.000-04:00

iGEM 2009 K.U.Leuven: Essencia coli, the fragrance factory. Promo video

2009-10-28T00:30:00.001-04:00

Video about how Essencia coli, the fragrance factory works. Visit their project's webpage at http://2009.igem.org/Team:KULeuven for more information.

IGEM 2009- Washington U Sunglasses for Sphaeroides

2009-10-28T00:00:00.000-04:00

This is an overview of the project done in 2009 by undergraduate students at Washington University in St. Louis participating in the iGEM competition. For more information, please visit: http://2009.igem.org/Team:Wash_U

Scientists Discover Gene That 'Cancer-proofs' Naked Mole Rat's Cells

2009-10-26T01:06:00.000-04:00

Quoted from: http://www.sciencedaily.com/releases/2009/10/091026152812.htm#at
ScienceDaily (Oct. 27, 2009) — Despite a 30-year lifespan that gives ample time for cells to grow cancerous, a small rodent species called a naked mole rat has never been found with tumors of any kind -- and now biologists at the University of Rochester think they know why. The findings, presented in The Proceedings of the National Academy of Sciences, show that the mole rat's cells express a gene called p16 that makes the cells "claustrophobic," stopping the cells' proliferation when too many of them crowd together, cutting off runaway growth before it can start. The effect of p16 is so pronounced that when researchers mutated the cells to induce a tumor, the cells' growth barely changed, whereas regular mouse cells became fully cancerous.
"We think we've found the reason these mole rats don't get cancer, and it's a bit of a surprise," says Vera Gorbunova, associate professor of biology at the University of Rochester and lead investigator on the discovery. "It's very early to speculate about the implications, but if the effect of p16 can be simulated in humans we might have a way to halt cancer before it starts."
Naked mole rats are strange, ugly, nearly hairless mouse-like creatures that live in underground communities. Unlike any other mammal, these communities consist of queens and workers more reminiscent of bees than rodents. Naked mole rats can live up to 30 years, which is exceptionally long for a small rodent. Despite large numbers of naked mole-rats under observation, there has never been a single recorded case of a mole rat contracting cancer, says Gorbunova. Adding to their mystery is the fact that mole rats appear to age very little until the very end of their lives.
Over the last three years, Gorbunova and Andrei Seluanov, research professor of biology at the University of Rochester, have worked an unusual angle on the quest to understand cancer: Investigating rodents from across the globe to get an idea of the similarities and differences of how varied but closely related species deal with cancer.
In 2006, Gorbunova discovered that telomerase -- an enzyme that can lengthen the lives of cells, but can also increase the rate of cancer -- is highly active in small rodents, but not in large ones.
Until Gorbunova and Seluanov's research, the prevailing wisdom had assumed that an animal that lived as long as we humans do needed to suppress telomerase activity to guard against cancer. Telomerase helps cells reproduce, and cancer is essentially runaway cellular reproduction, so an animal living for 70 years has a lot of chances for its cells to mutate into cancer, says Gorbunova. A mouse's life expectancy is shortened by other factors in nature, such as predation, so it was thought the mouse could afford the slim cancer risk to benefit from telomerase's ability to speed healing.
While the findings were a surprise, they revealed another question: What about small animals like the common grey squirrel that live for 24 years or more? With telomerase fully active over such a long period, why isn't cancer rampant in these creatures?
Gorbunova sought to answer that question, and in 2008 confirmed that small-bodied rodents with long lifespans had evolved a previously unknown anti-cancer mechanism that appears to be different from any anticancer mechanisms employed by humans or other large mammals. At the time she was not able to identify just what the mechanism might be, saying: "We haven't come across this anticancer mechanism before because it doesn't exist in the two species most often used for cancer research: mice and humans. Mice are short-lived and humans are large-bodied. But this mechanism appears to exist only in small, long-lived animals."
Now, Gorbunova believes she has found the primary reason these small animals are staying cancer-free, and it appears to be a kind of overcrowding early-warning gene that the naked mole rat expresses in its cells.
When Gorbunova and her team began specifically investigating mole rat cells, they were surprised at how difficult it was to grow the cells in the lab for study. The cells simply refused to replicate once a certain number of them occupied a space. Other cells, such as human cells, also cease replication when their populations become too dense, but the mole rat cells were reaching their limit much earlier than other animals' cells.
"Since cancer is basically runaway cell replication, we realized that whatever was doing this was probably the same thing that prevented cancer from ever getting started in the mole rats," says Gorbunova.
Like many animals, including humans, the mole rats have a gene called p27 that prevents cellular overcrowding, but the mole rats use another, earlier defense in gene p16. Cancer cells tend to find ways around p27, but mole rats have a double barrier that a cell must overcome before it can grow uncontrollably.
"We believe the additional layer of protection conferred by this two-tiered contact inhibition contributes to the remarkable tumor resistance of the naked mole rat," says Gorbunova in the PNAS paper.
Gorbunova and Seluanov are now planning to delve deeper into the mole rat's genetics to see if their cancer resistance might be applicable to humans.
This research was funded by the National Institutes of Health and the Ellison Medical Foundation.
Adapted from materials provided by University of Rochester.

Mesa Community College Biology 181 Fall 2009 Course Videos

2009-10-18T04:43:00.005-04:00

Dr. Dennis Wilson

COURSE - Biology 181 - August 26, 2009

COURSE - Biology 181 - August 28th, 2009

COURSE - Biology 181 - September 2nd, 2009

COURSE - Biology 181 - September 4th, 2009

COURSE - Biology 181 - September 9th, 2009

COURSE - Biology 181 - September 11th, 2009

COURSE - Biology 181 - September 16th, 2009

COURSE - Biology 181 - September 18th, 2009

COURSE - Biology 181 - September 23rd, 2009

COURSE - Biology 181 - October 7th, 2009

COURSE - Biology 181 - October 9th, 2009

COURSE - Biology 181 - October 14, 2009

More Lectures will be posted in the future: To see them go to http://www.youtube.com/user/mesacc#grid/user/DC901D5F2BFF60A9

The DIYbio Community - Presented at Ignite Boston 5 (2009)

2009-10-10T17:09:00.001-04:00

The DIYbio Community - Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.

"We founded diybio.org, a community for amateur scientists, last year in May, just in time to present at ignite boston 2008. Since then, the community has grown. In this talk, I spend 5 minutes giving a lighting overview of the community and the current hot projects members are working on: new, cheap, diy-hardware, distributed science experiments (think flashmobs for science), a biohacking coworking space, and some molecular biology experiments (including making genetically engineered fluorescent yogurt, a melamine biosensor, and a biological counter)." - Mac Cowell

Safety First!!! If you are a student working in a lab here are some additional safety videos to go along with your formal training

2009-10-10T14:08:00.003-04:00

This video series provides guidance and instruction on how to control risks associated with protocols and practices used in the modern biology laboratory. The series will make laboratory personnel aware of the intrinsic hazards associated with biomedical research and provide instruction in safe techniques that will enable workers to protect themselves from these hazards. The information will introduce new staff to good laboratory practices and provide meaningful technical review in safety for the more experienced laboratory worker.

Produced by Schumann Productions Inc. for the Howard Hughes Medical Institute Office of Laboratory Safety
© Howard Hughes Medical Institute

Chemical Storage Hazards from benny on Vimeo.

Glassware Washing Hazards from benny on Vimeo.

Centrifugation Hazards from benny on Vimeo.

Chemical Hazards from benny on Vimeo.

A list of iPhone apps every biologist needs

2009-10-10T05:41:00.000-04:00

Peruse a PhD student's top 10 smart phone applications that boost his efficiency and speed his research

Quoted from The Scientist Magazine: http://www.the-scientist.com/templates/trackable/display/news.jsp?type=news&o_url=news/display/56049&id=5604

By Balachandar Radhakrishnan

Although the desktop computer has long been the workhorse for modern scientists, it is high time for academics to embrace the next technological wave that is mobile computing. We have all been comforted by the efficiency with which today's computers allow us to process data and information. Now, emerging mobile computing platforms will allow researchers to access and manipulate information no matter where we are. The iPhone is a good example of a mobile device that can yield a substantial productivity boost for scientists. If you are an academic and use the iPhone or iPod Touch, here are the 10 apps that will benefit you most. Feel free to add apps that you like and use for your work in the comments.

1) Molecules
Molecules is an application for viewing 3D protein structures. Need to quickly look up a protein structure? Just pull up the Molecules app and browse through the Research Collaboratory for Structural Bioinformatics database, download the structure, and you're good to go.
Price: Free

2) Solutions
Solutions is an app from the programmers atMekentosj, who make nifty software tools for the "mac-a-demic." It's a must have calculator for making quick calculations required to prepare stock solutions and buffers. The app is very well designed, keeps lists of recently entered chemicals and their molecular weights, and has the ability to search for chemicals and their molecular weights in online databases.
Price: $2.99

3) Promega
Promega is a bundle of useful stuff from the Promega website thrown together as a handy iPhone app. This is mostly a web app, which means the application itself just provides an interface to the content on the Promega site. The BioMath calculators are the best part of the app. They help you handle conversions like μg to pmol, molar ratios of insert:vector concentrations, melting temperature calculations and more.
Price: Free

4) iCut DNA
Molecular biologists can typically remember the restriction sites of a couple of enzymes, but it's tough to memorize the sites for more than 10 or so. That's where iCut DNA comes in. This app brings New England Biolab's Restriction Enzyme Database (REBASE) of around 2000 enzymes onto your mobile device, allowing you to look up the recognition sequence of any type II restriction enzyme available on REBASE. The interface is seamless, and tracking down any enzyme is a snap. The app also lets you to select molecules based on enzyme name (with a handy auto-suggest drop down menu that narrows down enzymes based on your text input) or recognition sequence (again with auto-suggest drop down entries).
Price: $4.99

5) PubSearch Plus
PubSearch Plus gives you the ability to search PubMed from the comfort of your iPhone or iPod Touch, and lets you read and email selected publications. Though the iPhone screen isn't ideal for viewing high resolution images in research papers, it definitely helps when you're looking up a specific piece of information from a particular paper. The app also supports EZProxy so you can connect to journals that are available only through institutional access.
Price: $1.99

6) Papers
Papers is iTunes for research literature. Just as iTunes lets you sync your music with your iPod - the Papers app now has a companion app for the iPhone/iPod Touch that allows you to sync your collected journal papers. You can keep copies of all or some of your research papers on your mobile device for quick reading and reference. The built in pdf reader on the Papers app does the job comfortably and can be handled with versatile touch gestures. Papers also features "beaming" where users can send a pdf to another user or sync their library with a desktop wirelessly.
Price: $9.99

7) The Chemical Touch
The Chemical Touch is an app that brings a souped-up periodic table to the iPhone and iPod Touch. An additional table of amino acids is one of the most useful parts of the app. The 20 amino acids appear with their single letter and three letter codes, isoelectric point, RNA codons, etc.
Price: $0.99

8) Labtimer
Labtimer can be as useful in the lab as in the kitchen. As the name implies, it's a timer app that provides the feel of a conventional lab timer. There are four individual timers that can be set with corresponding text labels. The alarms on the app also play over any music that you may be listening to, making it useful even when you have your headphones in at the bench.
Price: Free

9) Evernote
Evernote, which started out as a simple note taking tool, is now a solid information manager that can handle everything from voice notes to clippings pulled from the web. The beauty of Evernote is its versatility. I frequently use Evernote to collect notes from meetings and whiteboards directly to my mobile device, adding voice memos for better clarity. It has helped make me more efficient, especially with its ability to sync with all the different devices on which I'm running Evernote. I take a note on my iPhone, and it gets automatically synced to my desktop at home, my notebook, my netbook, and my work PC.
Price: Free

10)RSS Reader
RSS feeds are essential tools for anybody who deals with information overload. As researchers we are always looking for information online, be it research publications, news articles, Journal TOCs or blog posts. A mobile RSS reader helps cut down on information clutter, and several are available for the iPhone and iPod Touch. I would recommend an app that can sync with an online service where your feeds are handled so that they can be accessed via the computer as well as your mobile device. Newsstand and Byline are two wonderful RSS reader apps that you should try.
Price: Byline $4.99, Newsstand $4.99

Balachandar Radhakrishnan is a PhD student at the University of Kassel, Germany, working on RNAi in the slime mold Dictyostelium. Bala has always been fascinated by technology, especially mobile technology and how it can help researchers in their endeavors. You can find more of his tips and advice here"

How high-throughput sequencing technologies are transforming biomedical research. Presented at UCLA CNSI, July 2009.

2009-10-10T05:38:00.000-04:00

Why High-Throughput Sequencing is Changing Almost Everything from Christopher Lee on Vimeo.

Thomas A. Steitz, 2009 Nobel Prize in chemistry winner, discusses his work.

2009-10-09T21:22:00.003-04:00

2009 Nobel Prize in chemistry winner Thomas A. Steitz, Sterling professor of Molecular Biophysics and Biochemistry and Professor of Chemistry at Yale.

Steitz is one of three winners for his work describing the structure and function of the ribosome, the protein making factory key to the function of all life.

Steitz, a Howard Hughes Medical Institute investigator, shares the $1.4 million award with Venkatraman Ramakrishnan of the MRC Laboratory of Molecular Biology, Cambridge, United Kingdom and Ada E. Yonath, Weizmann Institute of Science, Rehovot, Israel.

All three used a technology called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome. While the work began as a quest to answer basic questions about the makeup of ribosomes, knowledge of its structure has created targets for a new generation of antibiotics.

Eric Allen's Biochemistry Lectures

2009-10-09T12:57:00.000-04:00

Eric Allen's slides are simple and beautifully designed, and his commentary is direct and insightful. This is a great series for studying Biochemistry. Enjoy!

Overview of Biochemistry 28 Aug 2009

Overview of Biochemistry 28 Aug 2009 from Eric Allain on Vimeo.

Water Part 1, 2 Sept 2009

Water Part 1, 2 Sept 2009 from Eric Allain on Vimeo.

Water Part 2, 4 Sept 2009

Water Part 2, 4 Sept 2009 from Eric Allain on Vimeo.

Thermodynamics Part 2, 2 Sept 2009

Thermodynamics Part 2, 2 Sept 2009 from Eric Allain on Vimeo.

Carbohydrates Part 2, 11 Sept 2009

Carbohydrates Part 2, 11 Sept 2009 from Eric Allain on Vimeo.

Carbohydrates Part 3, 14 Sept 2009

Carbohydrates Part 3, 14 Sept 2009
from Eric Allain on Vimeo.

Proteins Primary Structure Part 1, 25 Sept 2009

Proteins Primary Structure Part 1, 25 Sept 2009 from Eric Allain on Vimeo.

Proteins Primary Structure Part 2, 28 Sept 2009

Proteins Primary Structure Part 2, 28 Sept 2009 from Eric Allain on Vimeo.

Proteins Primary Structure Part 3, 30 Sept 2009

Proteins Primary Structure Part 3, 30 Sept 2009 from Eric Allain on Vimeo.

Nucleotides and Nucleic Acids Part 1, 14 Spet 2009

Nucleotides and Nucleic Acids Part 1, 14 Spet 2009 from Eric Allain on Vimeo.

Nucleotides and Nucleic Acids Part 2, 16 Sept 2009

Nucleotides and Nucleic Acids Part 2, 16 Sept 2009 from Eric Allain on Vimeo.

Lipids and Biological Membranes, 16 Sept 2009

Lipids and Biological Membranes, 16 Sept 2009 from Eric Allain on Vimeo.

Amino Acids Part 1, 21 Sept 2009

Amino Acids Part 1, 21 Sept 2009 from Eric Allain on Vimeo.

Amino Acids Part 2, 23 Sept 2009

Amino Acids Part 2, 23 Sept 2009 from Eric Allain on Vimeo.

Protein Three Dimensional Structure Part 1, 2 Oct 2009

Protein Three Dimensional Structure Part 1, 2 Oct 2009 from Eric Allain on Vimeo.

Proteins Three Dimensional Structure Part 2, 5 Oct 2009

Proteins Three Dimensional Structure Part 2, 5 Oct 2009 from Eric Allain on Vimeo.

Proteins Three Dimensional Structure Part 3, 7 Oct 2009

Proteins Three Dimensional Structure Part 3, 7 Oct 2009 from Eric Allain on Vimeo.

Protein Function Myoglobin and Hemoglobin Part 1, 7 Oct 2009

Protein Function Myoglobin and Hemoglobin Part 1, 7 Oct 2009 from Eric Allain on Vimeo.

Introduction to Metabolism

Introduction to Metabolism from Eric Allain on Vimeo.

Glycogen Metabolism Part 1

Glycogen Metabolism Part 1 from Eric Allain on Vimeo.

Glucose Catabolism Part 2

Glucose Catabolism Part 2 from Eric Allain on Vimeo.

Glucose Catabolism Part 3

Glucose Catabolism Part 3 from Eric Allain on Vimeo.

Eric continues to post regularly, see his new videos by going to is Vimeo channel here... http://www.vimeo.com/eallain/videos/sort:newest

A wonderful interview with Mac Cowell about DIY BIO!

2009-10-02T09:43:00.000-04:00

Great work Mac!!! Awesome interview!

Innovation @ MIT

2009-09-22T10:52:00.000-04:00

Watch this at Boston.com

PUBLISHED: Wed, 17 Dec 2008
DESCRIPTION: This session features presentations and discussion around the alumni leadership conference's theme: Inspiring Innovation. Taking part in the session are Gururaj "Desh" Deshpande HM, Chairman, Sycamore Networks, A123 Systems, and Tejas Network; Subra Suresh ScD '81, P'10, Dean of the School of Engineering and Ford Professor of Engineering; and Randy Rettberg '70, principal research engineer, Department of Biological Engineering and Director of iGEM - the international Genetically Engineered Machine competition.

BBC Video - The Cell

2009-09-21T04:15:00.004-04:00

The Cell - The Spark of Life (Part 1/6)

The Cell - The Spark of Life (Part 2/6)

The Cell - The Spark of Life (Part 3/6)

The Cell - The Spark of Life (Part 4/6)

The Cell - The Spark of Life (Part 5/6)

The Cell - The Spark of Life (Part 6/6) (shows synthetic ribosome construction with Synthetic DNA machine and micro-pipetting action)

Drew Endy - Earth Sky 8 minute Interview

2009-09-21T03:38:00.002-04:00

I absolutely love the conceptual distinction Drew makes here between creation and construction. Excellent work Drew. This is the best answer I have heard so far to the perpetual "playing god" question.

Ted Talk (April 2009) Bonnie Bassler: The secret, social lives of bacteria

2009-08-31T23:59:00.000-04:00

The great thing about TED talks is that they are designed to take information and show why it has profound implications. This marriage of data and eureka, leads to the entertaining and engaging speeches TED is known for.

"Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves."

Synthetic Biology on KQED QUEST

2009-08-31T23:58:00.000-04:00

Apologies a million times for the lack of posting. Thanks to the troubled economy my day job is dominating my life right now, so I hardly have time to post. Thanks to everyone who keeps this blog going strong! We got over 90 visitors today!

Step by Step: How to Prepare a Slide of Cells

2009-08-31T23:54:00.000-04:00

"Middle and Secondary Level Biology: How to Prepare a Slide of Cells. This video details the step by step instructions of how to make a slide using cheek cells. Students learn the process of preparing and staining the slide for viewing and comparison. This is a classroom produced instructional science video intended for middle and secondary studies and homework help."

SchoolWAX TV VIDEO: The formation of Lipids

2009-08-31T23:47:00.001-04:00

SchoolWAX TV video: Glycolosis (10 enzymes that make possible the 10 steps in the breakdown of sugar)

2009-08-31T23:44:00.003-04:00

SchoolWAX TV VIDEO: The formation of Proteins

2009-08-31T23:41:00.002-04:00

SchoolWAX TV VIDEO: Great Animation/narration of the formation of Carbohydrate Bonds

2009-08-31T23:37:00.002-04:00

"This video describes the bonding structure of four elements in the periodic table (hydrogen, oxygen, nitrogen, and carbon) to form carbohydrates. This video is a part of the Cassiopeia collection, an effort to make science education videos available for free to anyone who wants them. The vision is that if a concept can be visualized, then understanding is not far behind. Each video is self-contained but also embedded in a larger science fiction story intended to generate interest in the sciences."

Leaf Pigmentosis (Leaf Pigment Chromatography)

2009-08-31T11:00:00.000-04:00

"his video is a lab cast created by John Sowash. It reviews a hands on biology project separating pigments in leaves through a process called chromatography. For resources related to this lab including student worksheets and teacher guides visit www.jrsowash.wikispaces.com/labcast"

Univeristy of Alberta iGEM Introduction Video

2009-07-30T23:18:00.000-04:00

IGEM Calgary - CTV and NUTV's Introduction

2009-07-30T23:16:00.004-04:00

Wow! CTV really kicked it up a notch compared to NUTV! :)

NUTV's report on IGEM Calgary

2009-07-30T23:16:00.001-04:00

iGEM/UCSF 2009 Three perspectives on iGEM a reseacher, a student, and a teacher

2009-07-30T23:14:00.001-04:00

Podcast: UK's Guardian Science Weekly

2009-07-30T22:44:00.001-04:00

http://download.guardian.co.uk/audio/kip/science/series/science/1247855895096/996/gdn.sci.090720.sc.science-weekly-podcast-synthetic-biology.mp3

Science Weekly: Rise of the biological machines
Synthetic biologist Paul Freemont describes a future in which purpose-built organisms will manufacture complex chemicals and drugs to order.

Synthetic Biology KQUED QUEST VIDEO

2009-07-30T22:28:00.002-04:00

PHYSORG ARTICLE: APOPTOSIS - Scientists provide important insight into apoptosis or programmed cell death

2009-07-14T23:07:00.003-04:00

But first, a refresher on A-POP-TO-SIS

Quoted from: http://www.physorg.com/news166786296.html:
A study by Nanyang Technological University (NTU)'s Assistant Professor Li Hoi Yeung, Assistant Professor Koh Cheng Gee and their team have made an important contribution to the understanding of the process that cells go through when they die. This process known as 'apoptosis' or programmed cell death, is a normal process in the human body which removes perhaps a million cells a second.

According to Professor Li, they discovered that during apoptosis, the cell's rescue mechanism is inhibited when certain proteins (i.e. 'anti-factors' that are necessary to keep a cell alive) are no longer able to enter the cell's nucleus, thus stopping the cell's ability to initiate its self-repair process.

In addition, they also discovered that the protein RanGTP, which is involved in the transportation of certain proteins into and out of the cell's nucleus, is reduced greatly during the early stages of apoptosis.

Under normal circumstances, there is a high distribution of RanGTP in the nucleus and a low concentration of RanGTP in the cytoplasm (the body enveloping the cell's nucleus). It is this gradient of RanGTP that exist across the nuclear-cytoplasmic boundaries that serves as a track and directs the transport of proteins and other molecules into and out of the nucleus. Hence, when the concentration of RanGTP is reduced in the nucleus, the RanGTP gradient collapses and the nuclear transport machinery subsequently shuts down.

Too little or too much apoptosis plays a role in a great many diseases. When programmed cell death does not work right, cells that should be eliminated may linger around and become immortal - for example, in cancer and leukemia. When apoptosis works overly well, it kills too many cells and inflicts grave tissue damage. This is the case in strokes and neurodegenerative disorders such as Alzheimer, Huntington and Parkinson diseases.

While it is established that cells undergo apoptosis when they are damaged by mechanical injury, exposed to death stimuli, or under stress, the mechanism that initiates apoptosis has not been comprehensively resolved. Thus the study by Professor Li, Professor Koh and their team at NTU have provided new insights on the process that cells go through while experiencing apoptosis.

And, from the Archives, here's some more info about apoptosis
Introduction lecture to apoptosis Xiaodong Wang, Apoptosis
A collection of videos about apoptosis: http://bio-alive.com/categories/apoptosis.htm
Full Text lab methodology papers on: Apoptosis (7)

Jen from Standford University shows us how to do DNA extraction from Strawberries

2009-06-21T12:16:00.010-04:00

An excellent first time project, that is completely safe, requires only a kitchen, and will give you visible DNA in a glass. And Jennifer is delightful! The video's are so easy to follow, they work for any level and any age group. Thanks Jen, This is great.

This article is from the Home Activities section of Stanford University's understanding genetics website: http://www.thetech.org/genetics/medicine.php
For your convenience it has been pasted below:

Do-It-Yourself Strawberry DNA (Kiwi's and Banana's work too)

Strawberries, bacteria, humans—all living things have genes, and all of these genes are made of DNA. That's why scientists can take a gene from one living thing and put it into another. For example, they can put human genes into bacteria to make new medicines.

How do scientists take DNA out of a living thing? It's not that hard—there are lots of ways to do it! You can follow the directions in the video above to get DNA out of a strawberry. Or you can follow the steps below. Either way you'll have strawberry DNA at the end!

What you need:

* measuring cup
* measuring spoons
* rubbing alcohol
* 1/2 teaspoon salt
* 1/3 cup water
* 1 tablespoon Dawn dishwashing detergent
* glass or small bowl
* cheesecloth
* funnel
* tall drinking glass
* 3 strawberries (green tops removed)
* reclosable plastic sandwich bags
* test tube or small glass jar (like the kind spices come in)
* bamboo skewer (find them at the grocery store)

What to do:

1. Chill the rubbing alcohol in the freezer. (You'll need it later.)
2. Mix the salt, water, and Dawn detergent in a glass or small bowl. Set the mixture aside. This is your extraction liquid.
3. Line the funnel with the cheesecloth, and put the funnel's tube into the glass.
4. Put the strawberries in the plastic bag and push out all the extra air. Seal it tightly.
5. With your fingers, squeeze and smash the strawberry mixture for 2 minutes.
6. Add 3 tablespoons of the extraction liquid you made in Step 2 to the strawberries in the bag. Push out all the extra air and reseal the bag.
7. Squeeze the strawberry mixture with your fingers for 1 minute.
8. Pour the strawberry mixture from the bag into the funnel. Let it drip into the glass until there is no liquid left in the funnel.
9. Throw away the cheesecloth and the strawberry pulp inside. Pour the contents of the glass into the test tube or small glass jar so it is 1/4 full.
10. Tilt the test tube or jar and very slowly pour the cold rubbing alcohol down the side. The alcohol should form a layer on top of the strawberry liquid. (Don't let the alcohol and strawberry liquid mix. The DNA collects between the two layers!)
11. Dip the bamboo skewer into the test tube where the alcohol and strawberry layers meet. Pull up the skewer. The whitish, stringy stuff is DNA containing strawberry genes!

You can try these steps to purify DNA from lots of other living things. Grab some oatmeal or kiwis from the kitchen and try it again! Which foods give you the most DNA?

And here's the DIY BIO NYC Group doing Strawberry DNA extraction in shot and wine glasses, and trying out a homemade gel electrophoresis box.

NYC's DIY BIO GROUP Insert Green Flourescent Protein Genes into DNA

2009-06-21T12:00:00.008-04:00

Using a kit developed for high school students, NYC DIY BIO transform E. coli with a plasmid carrying the gene for Green Fluorescent Protein (GFP). It's a little hard to understand at times, but the on screen titles help out. Great work NYC DIY BIO!

The work area met all criteria for Biosafety Level 1 as defined by the Centers for Disease Control.

In the last video they finish the transformation of E. coli with a plasmid containing the GFP (Green Fluorescent Protein) gene and succeed in generating green bacterial colonies. Next meeting we will purify the GFP and visualize it under black light and with gel electrophoresis.

For more info on GFP check out these archived posts:

1. BIO LAB EXPERIMENT WALK THROUGH VIDEOS - Mike White's Entire Collection - Inserting GFP into bacteria, Mixing Agar, and More!

2. Futures in Biotech 37: Just A Touch Of Green - Published on Dec 29, 2008 GREEN FLUORESCENT PROTEIN DISCOVERY and HOW ORGANISMS SENSE TOUCH
In these podcast's Marty Chalfie, the discoverer of GFP! Describes how he developed one of the most important tools of modern molecular biology, one that allows us to see inside a living cells, down to the protein level. With green fluorescent protein, or GFP, we can now track the life of a protein, from when the gene that makes the protein is turned on, to where it goes, to where it dies.

3. 11 Excellent Videos introducing GFP:

4. Green fluorescent protein Virtual Lab! Narrated in a flash classroom and Student Protocols are Included!

PSYORG Article: New tool isolates RNA within specific cells (w/Video)

2009-06-21T11:34:00.002-04:00

From PSYORG.com: http://www.physorg.com/news161861163.html

A team of University of Oregon biologists, using fruit flies, has created a way to isolate RNA from specific cells, opening a new window on how gene expression drives normal development and disease-causing breakdowns.

While DNA (deoxyribonucleic acid) provides an identical genetic blueprint in every cell, RNA
(ribonucleic acid) decodes genetic instructions that turn protein molecules on and off in different cell types.

The new tagging method, tested in a variety of subsets of Drosophila brain cells, is described in a paper put on line ahead of regular publication by the journal Nature Methods. Instead of scientists needing to physically separate cell types, they now can inject a chemically modified gene from the one-celled organism Toxoplasma gondii and activate it in only one cell type within a tissue. Only newly generated RNA in this cell type is then tagged and isolated. "By analyzing RNA from different cell types, we can begin to understand how cellular differences are generated," said lead author Michael R. Miller, a National Science Foundation-funded doctoral student in the lab of Chris Doe, a UO biologist and Howard Hughes Medical Institute (HHMI) investigator. "Our new TU-tagging method should be useful for isolating cell-type specific RNA from other organisms, including mammals, and should be useful in broad areas of research including studies of development, neurobiology and disease." The new non-toxic, non-invasive method makes it possible to "listen in" to the messages -- in fact, messenger RNA -- that the nucleus is sending each cell, without perturbing the cell, Doe said. "It is much like eavesdropping on a phone conversation, rather than pulling the person out of the house for questioning. The cell has no idea that its RNAs are being 'tagged' for isolation and study. That's good, because we get a more accurate idea of what the cell is saying."

That, Doe added, could be helpful for 'listening' to host cells before and after the initiation of a disease to determine how cells respond, or, for example study healthy immune cells versus bacterially-challenged immune cells or neurons before they learn a task and after they learn a task to determine what changes in the cell are caused by the experience. The new UO-developed tool builds on work led by co-author Michael D. Cleary, who as a doctoral student at Stanford University unveiled the T. gondii-based approach for use in analyzing RNA synthesis and decay in 2005 in Nature Biotechnology. Cleary, now a faculty member at the University of California, Merced, worked on the UO project as a postdoctoral fellowship funded by the National Institutes of Health and HHMI.

Cleary's group built its tool with the enzyme uracil phosphoribosyltransferase (UPRT), a nucleotide salvage enzyme that prepares nucleotides for incorporation into newly synthesized RNA. By altering the nucleotide analog 4-thiouracil, the UPRT enzyme caused RNA to become tagged with thiouracil (TU), allowing the "TU-tagged" RNA to be purified from untagged RNA. In Doe's lab, Miller, Cleary and research technician Kristin J. Robinson of the UO's institutes of Neuroscience and Molecular Biology manipulated Drosophila so that they would only express UPRT in specific target cells. The group tested the new approach in embryos, larvae and adults using microarray technology to detect cell type-specific gene expression. The researchers say the method should work in other systems, including vertebrates, by using gene transfer, retroviral delivery, electrical pulses of molecules through cell membranes, or messenger RNA injection. Source: University of Oregon

Drool Worthy! If money was no object. Amazing Lab Equipment

2009-06-21T09:00:00.000-04:00

This video released last month from QIAGEN, shows how many lab activities are becoming increasingly automated. Amazing...

$59 400x Zoom USB Microscope

2009-06-17T00:17:00.004-04:00

This is interesting. A 400x zoom USB from Celestron for 59$.

http://www.adorama.com/CNMSD.html

Here's the lens in action on youtube:

but it might be more trouble than its worth. It has be discontinued from the manufacturer - could be because of this...

Stormin Norman from Arizona on 4/3/2008 writes.

Pros:Quality Lenses, Strong Construction

Cons:Difficult to Use, Go from 20x to 400x hard, Sticky Zoom, Vibrates when focusing

"Is great to use but difficult to change from 20x to 400x. The manufacturer has a problem. Had to use pliers on the first one and broke a fingernail and the replacement was better but 400 x was still difficult to use and focus. Not like the one demonstrated at the CES in Las Vegas in January. "

Here's the demo Norman's talking about:

Anyone else have this?

NPR TODAY RADIO: Kay Aull discussing her home DNA Lab for genotyping her HFE gene

2009-06-16T23:42:00.005-04:00

Thanks to Jason Bobe on the DIYBIO mailing list letting us know about this...
23-year-old Kay Aull set up a do it yourself DNA lab in her closet! The MIT graduate says with just $300 and a little bit of knowledge, almost anyone can start combing through their DNA. She brings her lab equipment to our studio to show us how it all works.

CLICK HERE TO Listen

Windows Media Player:
mms://realserver.bu.edu:554/w/b/wbur/storage/2009/06/hereandnow_0616_4.wma

Real Player:
http://realserver.bu.edu:8080/ramgen/w/b/wbur/storage/2009/06/hereandnow_0616_4.rm

The Application of Platform-Based Design to Embedded Electronics and Synthetic Biological Systems (Video 2/26/2009)

2009-06-04T05:21:00.000-04:00

Watch Video
From the Series: CSE Colloquia - 2009 Produced by: University of Washington
02/26/2009

Description:
This talk will outline Platform Based Design techniques as they relate to both embedded electronics and synthetic biology. Platform-Based Design is a design methodology within Computer Aided Design which at its core promotes the separation of functionality from implementation. Rigorous and formal applications of PBD have been shown to be very useful in the design of embedded electronic systems. This work has manifested itself in the development of the Polis, Metropolis, and Metro II design environments at UC Berkeley. PBD's true power lies in its ability to cross into new application areas. Download Video as MP4

The Royal Academy of Engineering's MAY 2009 Report on Synthetic Biology

2009-06-03T04:41:00.004-04:00

Click here to download the PDF
"This report aims to define the term ‘synthetic biology’, review the state of the field and consider potential future developments and their likely technological, economic and societal impact. It will also attempt to assess the requirements for the development of the field and to identify key policy issues."

The following is a summary of the central themes and issues that the report
has investigated, and the resulting recommendations.

Defining synthetic biology
We define synthetic biology thus:
“Synthetic biology aims to design and engineer biologically based parts, novel
devices and systems as well as redesigning existing, natural biological systems.”
This definition, while maintaining a certain level of simplicity, expresses the key
aspects of synthetic biology. It is consistent with the views of most researchers
in the field (both in the UK and abroad) and those of The Royal Academy of
Engineering. Synthetic biology strives to make the engineering of biology easier and more predictable.

Current activity and applications
There is considerable activity in a number of areas including health, energy, the
environment, agriculture and applications in other industrial sectors.
A synthetic version of the anti-malarial drug artemisinin is being developed
using synthetic biology methods. This makes it amenable to large scale
industrial production - if successful, it will have a major impact on the
treatment of malaria in the developing world. The cost of treatment should be
low as the development of the drug is being funded by the Gates Foundation.

Journal Article (Free Full Text): Opportunities for microfluidic technologies in synthetic biology

2009-06-03T04:28:00.004-04:00

Opportunities for microfluidic
technologies in synthetic biology
"We introduce microfluidics technologies as a key foundational technology for synthetic biology experimentation. Recent advances in the field of microfluidics are reviewed and the potential of such a technological platform to support the rapid development of synthetic biology solutions is discussed." Published online before print May 27, 2009

Full TextFree
Full Text (PDF)Free

PSYORG Article: Stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome!

2009-05-31T23:49:00.004-04:00

Quoted from: http://www.physorg.com/news162753069.html May 28th
VIB researchers linked to K.U.Leuven and Harvard University show that stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome. They found that unstable pieces of junk DNA help tuning gene activity and enable organisms to quickly adapt to changes in their environments. The results will be published in the reputed scientific Journal Science.

Junk DNA

'Most people do not realize that all our genes only comprise about 3% of the total human genome. The rest is basically one large black box', says Kevin Verstrepen, heading the research team. 'Why do we have this DNA, what is it doing?'.

Scientists used to believe that most of the DNA outside of genes, the so-called non-coding DNA, is useless trash that has sneaked into our genome and refuses to leave. One commonly known example of such 'junk DNA' are the so-called tandem repeats, short stretches of DNA that are repeated head-to-tail. 'At first sight, it may seem unlikely that this stutter-DNA has any biological function', says Marcelo Vinces, one of the lead authors on the paper. 'On the other hand, it seems hard to believe that nature would foster such a wasteful system'.

Unstable repeats
The international team of scientists found that stretches of tandem repeats influence the activity of neighboring genes. The repeats determine how tightly the local DNA is wrapped around specific proteins called 'nucleosomes', and this packaging structure dictates to what extent genes can be activated. Interestingly, tandem repeats are very unstable - the number of repeats changes frequently when the DNA is copied. These changes affect the local DNA packaging, which in turn alters gene activity. In this way, unstable junk DNA allows fast shifts in gene activity, which may allow organisms to tune the activity of genes to match changing environments -a vital principle for survival in the endless evolutionary race.

Evolution in test tubes
To further test their theory, the researchers conducted a complex experiment aimed at mimicking biological evolution, using yeast cells as Darwinian guinea pigs. Their results show that when a repeat is present near a gene, it is possible to select yeast mutants that show vastly increased activity of this gene. However, when the repeat region was removed, this fast evolution was impossible. 'If this was the real world' the researchers say 'only cells with the repeats would be able to swiftly adapt to changes, thereby beating their repeat-less counterparts in the game of evolution. Their junk DNA saved their lives'.

Source: VIB (the Flanders Institute for Biotechnology)

CodeCon09 SynthBio Tutorial Handout

2009-05-23T13:28:00.002-04:00

Sung Won Lim recently posted this excellent resource on SynthBio from CodeCon 2009. Some of the data has already been posted on this blog, but here it is in a nice neat package.

      0000_DOWNLOAD_ALL_Co..> 19-Apr-2009 13:52   38M 
     01 Adventures in Syn..> 20-Aug-2008 18:49   11M 
     02 Foundations for e..> 08-Jun-2006 10:55  291K 
     03 Genetic parts to ..> 16-Aug-2007 12:34  451K 
     05 Setting the Stand..> 21-Aug-2008 08:27  408K 
     06 Refinement and St..> 21-Aug-2008 08:26  1.2M 
     07 Engineering BioBr..> 21-Aug-2008 08:29  407K 
     08 Synthetic biology..> 21-Jun-2007 14:58  510K 
     09 Laying the Founda..> 03-Apr-2009 16:00  141K 
     README - ANNOTATED B..> 18-Apr-2009 13:10  2.2K 
     appendix1 - Primer f..> 20-Aug-2008 12:49  5.5M 
     appendix2 - A Comput..> 12-Oct-2007 11:40  5.6M 
     appendix3 - GinkgoBi..> 18-Apr-2009 12:58   15M

A blog about building a DIY Lab inexpensively

2009-05-23T12:46:00.005-04:00

Here is a great blog that deals with trying to build a DIY lab very inexpensively. In it, Lawrence walks us through each step as he builds his own science lab. Thanks Lawrence!
http://citsci.blogspot.com/

Homemade Centrifuges
Converted Old Light Bulbs into Flasks
Homemade Oscilloscope
Parts For a MicroBio Lab
and more!

Synthetic Biology Resources

2009-05-23T12:25:00.001-04:00

http://syntheticbiology.org/
Image:SB Primer 100707.pdf
Berkeley Intro to Synthetic Biology (PDF)
Jason Kelly's Measurement Kit Video
Targeted Development of Registries of Biological Parts (Peccoud lab
Adventures in Synthetic Biology comic

Bioinformatics Tutorials Series (BITS)
A collaboration of the MIT Engineering and Science Libraries and Harvard's Countway Library

BIT 1.1: UCSC Genome Browser: Getting DNA Sequence (3:57)
BIT 1.2: UCSC Genome Browser: Using Annotation Tracks (5:47)
BIT 1.3: UCSC Genome Browser: Locating Intron-Exon Boundaries (4:56)
BIT 1.4: UCSC Genome Browser: Searching with BLAT (6:14)

BIT 2.1: Do I need to BLAST? The Use of BLAST Link (7:24)
BIT 2.2: Do I need to BLAST? The Use of Related Sequences (6:53)
BIT 2.3: Nucleotide BLAST (5:46)
BIT 2.4: Nucleotide BLAST: Algorithm Comparisons (6:14)

Posting Drought! Lack of Internet!

2009-03-16T10:57:00.003-04:00

I just moved into a new apartment and wont be able to post until I get a new internet connection installed. I will keep you posted. In the meantime you have over 100 SB 4.0 Conference Videos to go through so that should keep you busy! :)

SB 4.0 Videos have ARRIVED!!!!!!! (Synthetic Biology 4.0 conference Videos)

2009-03-13T00:01:00.001-04:00

It was worth the wait there are over a hundred videos!

Lauren Ha of the BBF and her colleagues from HKUST have uploaded ~110
videos from the SB4.0 conference, held in Hong Kong last October.

The videos are free online via:

http://www.youtube.com/user/BioBricksFoundation

The videos cover many different aspects of the conference, from formal
lectures to informal conversations.

About SB 4.0

The mission of Synthetic Biology 4.0 is to bring together researchers who are working to:

design and build biological parts, devices and integrated biological systems
develop technologies that enable such work
place this scientific and engineering research within its current and future social context

The conference was a coordinated effort between HKUST, Hong Kong University, and Chinese University. Hong Kong provided an ideal location to explore the commercialization of Synthetic Biology in Asia as well as the launching of regional research and educational programs. Further, the meeting facilitated connections between researches and leaders in government, industry, and civic organizations.

Reshma Shetty and Natalie Kuldell discuss do-it-yourself biology

2009-03-12T00:31:00.001-04:00

Natalie Kuldell
Reshma Shetty
January 14, 2009
Running Time: 1:10:47

Quoted from: http://mitworld.mit.edu/video/646

About the Lecture
Inspired by the vast potential of bioengineering, ordinary people are seeking their inner Frankenstein -- doctor, not monster. Two speakers who know their way around Petri dish and beaker discuss the possibilities and pitfalls of do-it-yourself biology with an MIT Museum crowd.

Showing ads from a 1980 Omni magazine, Natalie Kuldell reflects on the vast changes in computer engineering in the past few decades – from 20-lb PCs to laptops and handhelds. In contrast, she laments, genetic engineering today still resembles in large part its 1980 antecedents -- inserting bits of DNA into organisms like E. coli. She avers that computer engineering made such leaps because its technology was widely available to amateurs, who helped drive many advances. Biotech hasn’t moved as fast, and won’t, believes a nascent do-it-yourself (DIY) community, until basic components of biology become accessible to a larger population.

Synthetic biology aims to make new biological forms easier to engineer. Kuldell complains that “much of my time is spent doing things to do the experiments I need to do. It would be terrific not to have to build things in advance.” But building biological components and streamlining processes is difficult in biology, because biosystems are complex, and unpredictable. Can amateurs working with “Tupperware, thermometers and genetic engineering in the kitchen” discover “something remarkable doing their biology at home?”

Reshma Shetty thinks engineered organisms can do more than sense toxic metals in the environment or determine whether seawater is contaminated. She can “imagine a DIY bioengineer…doing something more fantastical, ambitious…. What about growing your own house?” Shetty describes a home experiment that can make bacteria smell like bananas. This is a small feat, but to achieve something significant, a real contribution to science, Shetty says DIY biologists need bio-engineered friendly organisms that will serve as common models, safe, easy to grow “and fun to use.” Candidates include moss, an easy to grow bacterium called Acinetobacter, and the salt-loving Halobacterium. By giving people the right tools, “they can build something fun and creative others can appreciate.”

Natalie Kuldell

Instructor of Biological Engineering, MIT

Natalie Kuldell did her doctoral and post-doctoral work at Harvard Medical School. She develops discovery-based curricula drawn from the current literature to engage undergraduate students in structured, reasonably authentic laboratory experiences. She has also written educational materials to improve scientific communication as it occurs across disciplinary boundaries and as it's taught in undergraduate subjects. Her research examines gene expression in eukaryotic cells, focusing most recently on synthetic biology and redesign of the yeast mitochondria. She serves as Associate Education Director for SynBERC, an NSF-funded research center for Synthetic Biology, and Councilor at Large for the Institute of Biological Engineering.

Reshma Shetty PhD '08

Founding Member, Ginkgo Bioworks

Reshma Shetty earned her MIT Ph.D. in Biological Engineering, where she engineered bacteria to smell like mint and banana. She has been active in the field for several years and co-organized SB1.0, the first international conference in synthetic biology in 2004. She spearheaded the use of OpenWetWare, a wiki for life science researchers, as an educational tool when she helped teach an MIT undergraduate laboratory course in synthetic biology in 2006. The course demonstrated how wiki’s can support university education and has served as a model for courses from institutions across the country. She also engineered bacteria to smell like mint and banana’s. Now she and four other MITers have founded a new synthetic biology startup called Ginkgo BioWorks.

Futures in Biotech 8: Drew Endy on Synthetic Biology (must listen! webcast from 2006)

2009-03-11T00:06:00.000-04:00

If you haven't heard this yet, it is an absolute must listen. It is from 2006 but it's a wonderful presentation from Drew. One of my favorites. The ability of Drew to dissect an argument down to it's core concepts makes my inner philosopher jump for joy. Sadly, I can't embed so you'll have to click here: http://www.twit.tv/fib8

J. Chris Anderson, asst. professor of bioengineering at UC Berkeley, leads a discussion on synthetic biology. (Feb 16th 2009 video)

2009-03-11T00:01:00.000-04:00

J. Chris Anderson, asst. professor of bioengineering at UC Berkeley, leads a discussion on synthetic biology. The discussion starts with a detailed overview of synthetic biology (and its distinction from genetic engineering). Chris then dives into the meat of his work, engineering E. Coli strains to target cancer cells.

Additional Resources
Chris’ Lab Page

C. Elegans Micro injection of GFP (Video)

2009-03-10T08:27:00.003-04:00

http://www.dnatube.com/video/687/C-elegans-micro-injection

Today is Cynthia Kenyon day! Her work has led to the discovery that the aging process is regulated by our genes! (video, webcast, and a summary)

2009-03-10T04:27:00.014-04:00

In 1993, Dr. Kenyon's discovery that a single-gene mutation could double the lifespan of C. elegans sparked an intensive study of the molecular biology of aging. Dr. Kenyon's findings have led to the discovery that an evolutionarily-conserved hormone signaling system influences aging in other organisms, including mammals. Kenyon has received many honors, including the King Faisal Prize for Medicine, the American Association of Medical Colleges Award for Distinguished Research, the Ilse & Helmut Wachter Award for Exceptional Scientific Achievement, and La Fondation IPSEN Prize, for her findings. She is a member of the U.S. National Academy of Sciences and the American Academy of Arts and Sciences. She is now the director of the Hillblom Center for the Biology of Aging at UCSF.

Cynthia Kenyon gives us an overview of her labs work:

"Aging and death are always with us. The sense of loss that comes with aging and death imbues the sonnets of Shakespeare, the stories of Oscar Wilde and the art of Cranach and others with great meaning and beauty. The idea of a fountain of youth is enchanting, but it has always been the stuff of fairy tales, not science. Scientists, too, think about aging, and they have been studying the aging process for a long time. But, like non-scientists, most of them have assumed that while it might be possible to live longer with a healthier lifestyle, nothing much could be done to fundamentally change the rate of aging.

Some of the most important discoveries in science have come not from studying people themselves, but from studying simpler creatures: bacteria, yeast, roundworms, fruit flies and mice. Although these animals look very different from one another and from people, they share universal mechanisms of life at the molecular level.

My lab has been studying a small microscopic roundworm called C. elegans for some time, and these animals are perfect for studies of aging because they get old and die in just a little over two weeks. What is more, it’s easy to look for genes that control virtually any process, simply by changing them (making mutations) and looking at the consequences.

It seemed to me that there was a good chance that the aging process, like so much else in biology, was not just a random and haphazard process but instead was subject to regulation by the genes. After all, rats live three years and squirrels can live for twenty-five, and these animals are different because of their genes. Also, most biological processes are subject to tight control by the genes. If so, then by finding genes that control aging, and then changing the activities of the proteins they encode, one day we might be able to stay young much longer than we do now.

When we began our studies of aging, in the early 1990s, one C. elegans gene that affected lifespan had been described, though it was poorly understood. When this gene was altered by a mutation, the animals lived 30-50% longer than normal. We looked for gene changes (mutations) that extended the lifespan of the roundworms, and we found that mutations in a gene called daf-2 doubled lifespan. These mutant worms still looked and acted young when they should be old. Seeing them was like talking to someone that looks 40 and learning that they were really 80. This was a stunning finding because no one thought it was possible. We also discovered another important gene, called daf-16, that was needed for this long lifespan. daf-16 was a gene that could keep an animal young.

We now know that these genes, daf-2 and daf-16, allow the tissues to respond to hormones that affect lifespan. We showed that daf-2 and daf-16 ultimately affect lifespan by influencing the activities of a wide variety of subordinate genes that influence the level of the body’s antioxidants, the power of its immune system, its ability to repair its proteins, and many other beneficial processes. We have found that the activity of the youthfulness gene daf-16 is influenced by signals from the environment and also by signals from within - from its reproductive system. This knowledge has now allowed us to extend the lifespan of active, youthful worms by six fold.

Others have now extended these findings to show that daf-2-like genes control the lifespan of fruit flies, mice and possibly (from studies that will be published soon) also humans. When these genes are changed, aging is slowed and lifespan is extended.

Especially wonderful is the fact that these long-lived animals are resistant to a variety of age related diseases, including (in various animals) cancer, heart failure, and protein-aggregation disease. Thus these mutants not only look young, they are young, in the sense that they are not susceptible to age-related disease until later. (Many people assume that if you could delay aging, you would just die of Alzheimer’s disease. We don’t know for sure, but this may not be true if ‘being elderly’ is what makes one susceptible to Alzheimer’s disease.) This link between aging and age-related disease suggests an entirely new way to combat many diseases all at once; namely, by going after their greatest risk factor: aging itself. This is an extremely exciting and important concept that could revolutionize medicine, human health and longevity, and it has just now begun to be studied in earnest, still in only a handful of labs.

Because it is very easy to look for genes affecting lifespan in C. elegans, we are continuing to do that in our lab. In fact, you can think of C. elegans as a ‘fountain of youthfulness genes’. We have identified about fifty genes so far that affect lifespan, and others have found this type of gene as well. More importantly, we are now using all the powerful molecular techniques available for studying this little animal to figure out just what these genes do to affect lifespan, so that we can apply that knowledge in a rational way. Whether these genes have universal effects on lifespan can now be tested in higher animals, where it is harder to discover lifespan genes starting from scratch. With all this new information, pharmaceutical and biotech companies can now make drugs that influence the activities of the proteins encoded by these genes, in hopes of combating age-related disease, and possibly aging itself, in humans. We don’t know yet, but to me it seems possible that a fountain of youth, made of molecules and not simply dreams, will someday be a reality."

To hear more from Cynthia Kenyon you can listen to her interview with Marc Pelletier on the webcast, Futures in Biotech 36: Avoiding Death, Not Taxes with Dr. Cynthia Kenyon Published on Nov 24, 2008

Host: Marc Pelletier Guest: Dr. Cynthia Kenyon; Professor, Department of Biochemistry and Biophysics, University of California San Francisco, Director of the Larry L. Hillblom Center for the Biology of Aging. We are back into a world leading lab to discuss the genetics of aging. Can it be controlled? You bet, and the implications are enormous. When these findings translate to the clinic, it will truly be a game changer for humanity.

You can also hear Cynthia Kenyon's American Society for Cell Biology iBio Seminar on Aging here: Cynthia Kenyon, Mechanisms of Aging

And if you haven't seen it already, make sure to check out her discussion at the 2007 Aspen Health Forum: "Science vs the Biological Clock"
William Colby, Cynthia Kenyon and Stephanie Lederman all discuss the process of aging:
http://diybio4beginners.blogspot.com/2009/02/science-versus-biological-clock-video.html

INTRO TO CADHERINS AND INTEGRINS - THE GLUE THAT STOP US FROM BEING GOO! (Videos + Seed Magazine Article)

2009-03-10T01:00:00.000-04:00

Cadherins (Calcium dependant adhesion molecules) are a class of type-1 transmembrane proteins. They play important roles in cell adhesion, ensuring that cells within tissues are bound together. They are dependent on calcium (Ca²⁺) ions to function, hence their name.

Excellent Videos about Cadherins (I was not able to embed the videos so click on the links below):
Cadherins: Structure and Function Part I ( introduction)
Cadherins: Structure and Function Part II ( Cadherin Molecular Structure and Function )
Cadherins: Structure and Function Part III ( Adherens Junctions and Tissue Morphogenesis )
Cadherins: Structure and Function Part IV ( Cadherins in the Neural Network )
Cadherins: Structure and Function Part V ( Conclusion )

EXCERPT from Seed Magazine article: The Mason's Apprentice
http://www.seedmagazine.com/news/2008/10/the_masons_apprentice_1.php

"Multicellularity requires complex cell adhesion and signaling abilities — development and differentiation cannot occur without them. A multicellular organism is made up of cells that stick to one another with varying degrees of strength, which is mediated by an external coat of proteins and sugars that makes cells sticky in specific ways. In addition, cells secrete proteins and sugars that form a kind of fibrous goo called the extracellular matrix, to which they can also stick. When cell proteins bind to other cells or the extracellular matrix, the proteins trigger biochemical changes — the signaling part of the process — that can cause changes in cell metabolism, gene activity, cell shape, and physiology. These capabilities are fundamental to building a multicellular organism.

So where did they come from?

One must be careful when investigating this question not to make an easy but erroneous assumption: that cell adhesion and cell-to-cell signaling are a consequence of multicellularity. They are not. In fact, it turns out that single-celled organisms have a diverse array of mechanisms for interacting with one another, and multicellular life's fancy cell-communication tools are recent appropriations of mechanisms refined by evolution over billions of years, well before the first tiny worm congealed in the late pre-Cambrian.

"Simple" one-celled organisms like bacteria (which aren't simple, except in terms of number of cells) are sensitive to their environment, including the presence of other bacteria, and transduce chemical signals around them into changes in gene activity. The central principles of cell signaling are all in place in E. coli, and we can see the general idea clearly expressed in the rest of the prokaryotes. But another group of single-celled organisms, a group of eukaryotes — are of particular interest to multicellular animals like ourselves because they are the protists most closely related to us. These organisms are pf great interest to evolutionary biologists because they demonstrate that our toolbox of cell-adhesion and signaling proteins are of utility to organisms that don't have tissues and a higher level of organization. These fascinating creatures are the choanoflagellates.

Two particularly significant classes of proteins that animals use for adhesion and signaling are shared between animals and choanoflagellates. One is a group of proteins called cadherins. These are important cell-adhesion molecules that are regulated by calcium in the environment. Before being found in choanoflagellates, cadherins were thought to be unique to animals — plants and fungi do not have them. Another is a group of proteins called integrins that help cells stick to the extracellular matrix. Among other things, these molecules adhere to the collagen in connective tissues; they are essential for holding us together in a coherent form, versus a pile of gooey jelly."

Wiki:
Cadherins are a class of type-1 transmembrane proteins. They play important roles in cell adhesion, ensuring that cells within tissues are bound together. They are dependent on calcium (Ca²⁺) ions to function, hence their name. The cadherin superfamily includes cadherins, protocadherins, desmogleins, and desmocollins, and more. In structure, they share cadherin repeats, which are the extracellular Ca²⁺-binding domains.

There are multiple classes of cadherin molecule, each designated with a prefix (generally noting the type of tissue with which it is associated). It has been observed that cells containing a specific cadherin subtype tend to cluster together to the exclusion of other types, both in cell culture and during development. For example, cells containing N-cadherin tend to cluster with other N-cadherin expressing cells. However, it has been noted that the mixing speed in the cell culture experiments can have an effect on the extent of homotypic specificity.^[1] In addition, several groups have observed heterotypic binding affinity (i.e., binding of different types of cadherin together) in various assays.^[2]^[3] One current model proposes that cells distinguish cadherin subtypes based on kinetic specificity rather than thermodynamic specificity, as different types of cadherin homotypic bonds have different lifetimes.^[4]

Different members of the cadherin family are found in different locations. E-cadherins are found in epithelial tissue; N-cadherins are found in neurons; and P-cadherins are found in the placenta. T-cadherins have no cytoplasmic domains and must be tethered to the plasma membrane.

E-cadherin (epithelial) is the most well-studied member of the family. It consists of 5 cadherin repeats (EC1 ~ EC5) in the extracellular domain, one transmembrane domain, and an intracellular domain that binds p120-catenin and beta-catenin. The intracellular domain contains a highly-phosphorylated region vital to beta-catenin binding and therefore to E-cadherin function. Beta-catenin can also bind to alpha-catenin. Alpha-catenin participates in regulation of actin-containing cytoskeletal filaments. In epithelial cells, E-cadherin-containing cell-to-cell junctions are often adjacent to actin-containing filaments of the cytoskeleton.

E-cadherin is first expressed in the 2-cell stage of mammalian development, and becomes phosphorylated by the 8-cell stage, where it causes compaction. In adult tissues, E-cadherin is expressed in epithelial tissues, where it is constantly regenerated with a 5-hour half-life on the cell surface.

Loss of E-cadherin function or expression has been implicated in cancer progression and metastasis. E-cadherin downregulation decreases the strength of cellular adhesion within a tissue, resulting in an increase in cellular motility. This in turn may allow cancer cells to cross the basement membrane and invade surrounding tissues.

Another is a group of proteins called integrins that help cells stick to the extracellular matrix.

Heat Stress Causes Bacterial Forsight - SEED MAGAZINE Article

2009-03-10T00:01:00.000-04:00

Quoted from Seed Magazine. See the original article here:
http://www.seedmagazine.com/news/2008/10/bacterial_foresight.php

Can bacteria anticipate changes in their environment?

The homeostatic framework has long dominated the study of bacteria and microbiology, asserting that bacteria change their behavior based on the information they receive from their local environment. Researchers know, for example, that when E. coli bacteria enter the gut — an environment lacking oxygen — they switch to a form of anaerobic respiration in order to survive.

But there is a fundamental problem for any organism that behaves only by reacting to its environment after the fact: The behavior is not very efficient. If bacteria had the ability to use environmental cues to plan for future changes, the transition would be far smoother, and their survival more assured.

A group of microbiologists studying E. coli recently noted that before entering the deoxygenated gut, the bacteria enter the mouth and experience a rise in temperature. When the researchers exposed the bacteria to a similar increase in temperature, as if in anticipation of entering the gut, they found that E. coli turned to anaerobic respiration even without oxygen deprivation.

Convergence: Synthetic Biology Panel (2008 video)

2009-03-09T12:17:00.002-04:00

(Part 1 of 2)

Convergence: Synthetic Biology Panel (Part 1 of 2) from Jeriaska on Vimeo.

(Part 2 of 2)

Convergence: Synthetic Biology Panel (Part 2 of 2) from Jeriaska on Vimeo.

About the speakers:
Chris Anderson is a bioengineering researcher and educator. He received his Ph.D. in 2003 from the Scripps Research Institute for expanding the genetic code through genetic engineering. Currently he is a professor in the Department of Bioengineering at UC Berkeley. His research focuses on foundational technologies and applications of synthetic biology, a ground-up approach to genetic engineering with diverse applications in healthcare, environmental remediation, bioenergy, chemicals and materials production. Chris is best known for his ongoing work on developing therapeutic bacteria for the treatment of cancer for which he was recognized with Technology Review's TR35 award in 2007.

Denise Caruso co-founded the nonprofit Hybrid Vigor Institute in 2000 to study and practice collaboration in the service of new solutions for complex social and scientific problems. She recently published Intervention: Confronting the Real Risks of Genetic Engineering and Life on a Biotech Planet, and continues to work on projects both in academia and the private sector to improve the practice of risk analysis for science and technology-related innovations. For the five years prior to founding Hybrid Vigor, Denise wrote the Technology column for the Monday Information Industries section of The New York Times.

Gregory Benford is a physicist, educator, and author. He received his Ph.D. in 1967 from UC San Diego. Benford is a professor of physics at UC Irvine, where he has been a faculty member since 1971. He conducts research in plasma turbulence theory and experiment, and in astrophysics. He has published over a hundred papers in fields of physics from condensed matter, particle physics, plasmas and mathematical physics, and several in biological conservation. He is a Woodrow Wilson Fellow at Cambridge University, and has served as an advisor to the Department of Energy, NASA and the White House Council on Space Policy. In 1995 he received the Lord Foundation Award for contributions to science and the public comprehension of it. He is the author of over 20 novels, including Jupiter Project, Artifact, Against Infinity, and Timescape. He is a two-time winner of the Nebula Award.

Andrew Hessel, MSc, iGEM Program Development, Alberta Ingenuity Fund, is a biologist and author working to promote synthetic biology and open source biology. In his view, synthetic biology allows forward engineering, permitting scientists to write code de novo, and allowing logical, fully understandable evolution of biological outputs ranging from single proteins to synthetic bacteria. Andrew advocates the use of open source principles for creating DNA code. He believes open biology could potentially create a more diversified and sustainable biotechnology industry.

DIY BIO COMMUNITY OVERVIEW IN 4 MINS WITH MAC COWELL

2009-03-09T12:00:00.002-04:00

The DIYbio Community - Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.

Quoted from diybio.org...
"We founded diybio.org, a community for amateur scientists, last year in May, just in time to present at ignite boston 2008. Since then, the community has grown. In this talk, I spend 5 minutes giving a lighting overview of the community and the current hot projects members are working on: new, cheap, diy-hardware, distributed science experiments (think flashmobs for science), a biohacking coworking space, and some molecular biology experiments (including making genetically engineered fluorescent yogurt, a melamine biosensor, and a biological counter)."

Mac's first video at O'Reilly Ignite Boston 2008:

DIYbio in 5 minutes - O'Reilly ignite Boston from mac cowell on Vimeo.

AGBT 2009 – Notes (Sadly I could find no other videos)

2009-03-08T00:45:00.003-05:00

Here is a collection of notes, thoughts, and reflections on AGBT 2009 by Anthony Fejes. You can visit his blog at the link below:
http://www.fejes.ca/labels/AGBT%202009.html

Next-Generation Informatics - Fresh Video from Feb 2009 AGBT conference

2009-03-08T00:35:00.007-05:00

David Dooling recreates the talk he gave in the Bioinformatics session at AGBT 2009.

2009 AGBT Meeting

"The 10th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 4-7, 2009. The AGBT meeting has become the premier scientific forum for capturing the latest advances in new DNA sequencing technologies and an outstanding venue for presentations on the applications of genomics to diverse areas in biology and biomedicine."

Microbiology Video Encyclopedia

2009-03-08T00:30:00.002-05:00

http://www.microbiologybytes.com/video/videoindex.html

Biology Prefixes and Suffixes

2009-03-08T00:01:00.001-05:00

Biology Prefixes and Suffixes that start with A or B are below... you can find the rest of the alphabet here: http://biology.about.com/od/prefixesandsuffixes/a/aa020106a.htm

A and B

SUFFIX
-ase = enzyme
Examples: sucrase (sucr-ase) - an enzyme that catalyzes the decomposition of sucrose into glucose and fructose

-ate = having, characterized by, resembling
Examples: nervate (nerv-ate) - leaves characterized by prominent veins

-ary = of or relating to
Examples: urinary (urin-ary) - of or relating to urine and its production or excretion

PREFIX
auto- = self. Examples: autotroph (auto-troph) - organism that is self nourishing or capable of generating its own food

asco- = sac, bag. Examples: ascomycete (asco-mycete) - fungi whose spores are produced in a sac

arth- = joint. Examples: arthritis (arth-itis) - joint inflammation

antho- = flower. Examples: anthophyta (antho-phyta) - plant division composed of flowering plants

ante- = before. Examples: antemortem (ante-mortem) - before death

angio- = vessel. Examples: angiotensin (angio-tensin) - neurotransmitter that causes blood vessels to become narrow

andro- = male. Examples: androgen (andro-gen) - male hormone

ana- = upward, back, again. Examples: anaplasia (ana-plasia) - cell reverting to an immature form

-amyl = starch. Examples: amylase (amyl-ase) - a group of starch enzymes

amphi- = both, on both sides, around. Examples: amphibian (amphi-bian) - animal that can live on both land and water

ambi- = both. Examples: ambidextrous (ambi-dextrous) - capable of using both hands

aer- or aero- = air, oxygen. Examples: aerobic (aer-o-bic) - with oxygen

ad- = toward, near. Examples: adrenal (ad - renal) - toward the kidneys

ab- = away from. Examples: abnormal (ab - normal) - departing from normality

a- = without, negative, not. Examples: asexual ( a- sexual) - without sex

bi- = two. Examples: biennial (bi-ennial ) - plant with two year life span

bio- = life. Examples: biology (bio-logy) - the study of life

brachio- = upper arm, forelimb. Examples: brachium (brachi-um) - arm-like part of an animal

brady- = slow. Examples: bradycardia (brady-cardia) - slow heart beat

bronchi- = windpipe. Examples: bronchioles (bronchi-oles) - small tubes in the lungs

bryo- = moss. Examples: bryophyte (bryo-phyte) - mosses

-blast = bud or germ. Examples: osteoblast (osteo-blast) - a cell from which bone is derived

FOR C-Z click here -> http://biology.about.com/od/prefixesandsuffixes/a/aa020106a.htm

The ecosystem that is your mouth! The Human Oral Microbiome by Floyd Dewhirst, Harvard University

2009-03-07T08:13:00.004-05:00

"The human oral cavity is a diverse habitat that contains approximately bacterial 600 predominant species. The oral microbiome is comprised of 44% named species, 12% isolates representing unnamed species, and 44% phylotypes known only from 16S rRNA based cloning studies. Species from 11 phyla have been identified: Firmicutes (211), Bacteroidetes (106), Proteobacteria (99), Actinobacteria (64), Spirochaetes (49), Fusobacteria (29), TM7 (12), Synergistetes (10), Chlamydiae (1), Chloroflexi (1) and SR1(1). Full and survey sequences have been obtained for over 30 oral species, and in the course of the Human Microbiome Project over 300 essentially complete genome sequences should be determined. An Oral Microbiome Project is in progress and data from this project should be available soon. The talk will discuss the diversity of the oral microbiome, the Human Oral Microbiome Database (a resource for exploring the Oral Microbiome), and efforts to connect the oral metagenome with the oral metaproteomics and structural metagenomics."

The ecosystem that is your stomach! Genomic and Genetic Insight into Gut Microbiota Function and Manipulation

2009-03-07T00:09:00.003-05:00

"Trillions of microbes live in our digestive tract and influence our biology in profound and diverse ways. Several diseases, including obesity and inflammatory bowel diseases, have been associated with large-scale shifts in microbiota composition. The ability to address basic questions concerning community function and plasticity are fundamental to understanding the extent of causal relationships between host biology and microbiota perturbations, and whether the microbiota is a viable therapeutic target. One of our long-term goals is to achieve a level of functional understanding that, if provided the metagenome of an individual’s microbiota, would allow us to accurately predict how the microbial community will functionally adapt to a specific perturbation (e.g., dietary change). To investigate how changes in the intestinal environment alter microbiota function, and how these changes, in turn, influence host biology we have characterized responses of simplified microbiotas living within the gut of gnotobiotic mice to changes in host diet, community membership, and host genotype. These studies have revealed the importance of a finely-tuned system of polysaccharide sensing and utilization in the model symbiont Bacteroides thetaiotaomicron (B. theta). We are currently using a single polysaccharide utilization locus dedicated to dietary fructan utilization of B. theta as a model to understand mechanisms underlying diet-induced changes in microbiota function and composition. Genetic ablation of proteins involved in the multi-step process of sensing, harvesting, degrading, and metabolizing fructans variably cripples B. theta’s utilization of fructose-based polysaccharides depending upon which step of consumption is compromised. These findings are consistent with functional differences in fructan utilization between Bacteroides species. Together these results set the stage for predicting, based on gene content, how microbiotas respond to changes in the nutrient environment and suggest how metagenomics could facilitate personalized therapeutic manipulation of the microbiota."

A proposal for a field guide for microbes just like a field guide for birds. "A Genomic Encyclopedia of Bacteria and Archaea (GEBA)"

2009-03-07T00:00:00.005-05:00

"There is a glaring gap in microbial genome sequence availability – the currently available genome sequences show a highly biased phylogenetic distribution compared to the extent of microbial diversity known today. This bias has resulted in major limitations in our knowledge of microbial genome complexity and our understanding of the evolution, physiology and metabolic capacity of microbes. Although there have been small efforts in sequencing genomes from across the tree of life for microbes, there are no systematic efforts. There are many reasons why phylogenetic based sequencing in theory should be of great benefit including: (a) improved identification of protein families and orthology groups across species, which will improve annotation of other microbial genomes (b) improved phylogenetic anchoring of metagenomic data, (c) gene discovery (which tends to be maximized by selecting phylogenetically novel organisms, (d) a better understanding of the processes underlying the evolutionary diversification of microbes (e.g., lateral gene transfer and gene duplication) (e) a better understanding of the classification and evolutionary history of microbial species and (f) improved correlations of phenotype and genotype in microbes. Based on the potential benefits, we (JGI) have commenced a pilot project to create a Genomic Encyclopedia of Bacteria and Archaea (GEBA). In this pilot, we plan to sequence ~100 genomes selected based on their phylogenetic novelty. This is being done at two phylogenetic scales. About 60 of the genomes are from across the breadth of bacteria and archaea. The remaining 40 genomes are from within the Actinobacteria. By doing this two tiered selection we can test both the value of breadth from across the bacteria and archaea as well as the value of filling in the phylogenetic gaps within a single phyla. In my talk I will summarize the project and report on the sequencing and analysis of the first 56 genomes. I will discuss how we are using this pilot to test protocols that could be used for a scale up of the GEBA project or for any other large scale microbial sequencing project. In addition I will discuss how collaborations with culture collections can be valuable in such a project. Finally, I will report on the results of tests of the value of phylogenetic based sequencing."

A trip through some of the phylums of life: The biology of chordates, annelids, and cnidarians

2009-03-06T11:02:00.001-05:00

Biology of chordates

Biology of annelids.

Biology of cnidarians

Dave Issadore over at Harvard explains integrated circuts and shows you how he made cells do the waltz!

2009-03-05T01:17:00.003-05:00

To learn more, check out their lab on a chip paper:
http://www.rsc.org/Publishing/Journals/LC/article.asp?DOI=b710928h

Duke University: Lab-on-a-chip 1 minute Demo

2009-03-05T01:04:00.002-05:00

Dr. Jiang explains Lab-on-a-chip! Here he talks about controlled Microfluidic Interfaces for Microoptics and Microsensing (Video 2008 September)

2009-03-05T01:00:00.003-05:00

EECS Department Colloquium (EECS 500) Hongrui Jiang, Ph.D.
"Controlled Microfluidic Interfaces for Microoptics and Microsensing"
September 11, 2008 Lab on a chip has found many applications in biological and chemical analysis. Because these labs on chips involve handling of fluids at the microscale, surface tension profoundly affects the behavior and performance of these systems.

Recombinant DNA

2009-03-05T00:35:00.000-05:00

A 3D animation illustrating the process by which a protein is mass-produced using spliced DNA and bacterial replication.

Intro to the Biology of Algea (Video 1998 or older)

2009-03-04T07:54:00.005-05:00

Intro to the Biology of Bacteria (Video 1999)

2009-03-04T07:28:00.000-05:00

Intro to the biology of plants (Video 1997) - Warning 90's era video

2009-03-04T07:01:00.001-05:00

An overview of the process of photosynthesis and the biology of plants - function, reproduction and life.

Researchers make stem cell breakthrough - STEM CELLS WITHOUT EMBRYOS!

2009-03-03T14:17:00.004-05:00

QUOTED FROM: PSYSORG.com http://www.physorg.com/news155138024.html

"This new method of generating stem cells does not require embryos as starting points and could be used to generate cells from many adult tissues such as a patient's own skin cells." - Dr. Nagy, Senior Investigator at the Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Investigator at the McEwen Centre for Regenerative Medicine, and Canada Research Chair in Stem Cells and Regeneration.

Dr. Nagy discovered a new method to create pluripotent stem cells (cells that can develop into most other cell types) without disrupting healthy genes. Dr. Nagy's method uses a novel wrapping procedure to deliver specific genes to reprogram cells into stem cells. Previous approaches required the use of viruses to deliver the required genes, a method that carries the risk of damaging the DNA. Dr. Nagy's method does not require viruses, and so overcomes a major hurdle for the future of safe, personalized stem cell therapies in humans.

"This research is a huge step forward on the path to new stem cell-based therapies and indicates that researchers at the Lunenfeld are at the leading edge of regenerative medicine," said Dr. Jim Woodgett, Director of Research for the Samuel Lunenfeld Research Institute of Mount Sinai Hospital. Regenerative medicine refers to enabling the human body to repair, replace, restore and regenerate its own damaged or diseased cells, tissues and organs.

The research was funded by the Canadian Stem Cell Network and the Juvenile Diabetes Research Foundation (United States).

Dr. Nagy joined Mount Sinai Hospital as a Principal investigator in 1994. In 2005, he created Canada's first embryonic stem cell lines from donated embryos no longer required for reproduction by couples undergoing fertility treatment. That research played a pivotal role in Dr. Nagy's current discovery.

One of the critical components reported in Nagy's paper was developed in the laboratory of Dr. Keisuke Kaji from the Medical Research Council (MRC) Centre for Regenerative Medicine at the University of Edinburgh. Dr. Kaji's findings are also published in the March 1, 2009 issue of Nature. The two papers are highly complementary and further extend Nagy's findings.

"I was very excited when I found stem cell-like cells in my culture dishes. Nobody, including me, thought it was really possible," said Dr. Kaji. "It is a step towards the practical use of reprogrammed cells in medicine."

Source: Samuel Lunenfeld Research Institute

Understanding the classification of life: What is a Phylum?

2009-03-03T09:01:00.004-05:00

WIKI: A phylum (plural: phyla)^{[note 1]} is a taxonomic rank below Kingdom and above Class. "Phylum" is equivalent to the botanical term division.^[1]

Although a phylum is often spoken of as if it were a hard and fast entity, no satisfactory definition of a phylum exists. Consequently the number of phyla varies from author to author. The relationship of phyla is increasingly well known, and larger clades can be erected to contain many of the phyla.

Informally, phyla can be thought of as grouping animals based on general body plan,^[2] developmental or internal organizations.^[3] For example, though seemingly divergent, spiders and crabs both belong to Arthropoda, whereas earthworms and tapeworms, similar in shape, are from Annelida and Platyhelminthes, respectively. Although the International Code of Botanical Nomenclature allows the use of the term "phylum" in reference to plants, the term "Division" is almost always used by botanists.

The best known animal phyla are the Mollusca, Porifera, Cnidaria, Platyhelminthes, Nematoda, Annelida, Arthropoda, Echinodermata, and Chordata, the phylum to which humans belong. Although there are approximately 35 phyla, these nine include over 96% of animal species. Many phyla are exclusively marine, and only one phylum, the Onychophora (velvet worms) is entirely absent from the world's oceans–although ancestral oncyophorans were marine.^[4]

MARINE BIO: INTRO TO Echinoderms (Phylum: Echinodermata)

2009-03-03T08:37:00.001-05:00

WIKI: Echinoderm
Fossil range: Cambrian - present
Domain: Eukaryota
Kingdom: Animalia
Subkingdom: Eumetazoa
Superphylum: Deuterostomia
Phylum: Echinodermata

Echinoderms (Phylum Echinodermata) are a phylum of marine animals (including sea stars). Echinoderms are found at every ocean depth, from the intertidal zone to the abyssal zone. Aside from the problematic Arkarua, the first definitive members of the phylum appeared near the start of the Cambrian period. The phylum contains about 7,000 living species, making it the second-largest grouping of deuterostomes, after the chordates; they are also the largest phylum that has no freshwater or terrestrial representatives. The word derives from the Greek εχινοδέρματα (echinodermata), plural of εχινόδερμα (echinoderma), "spiny skin" and that from εχινός (echinos), "sea-urchin", originally "hedgehog"[1] + δέρμα (derma), "skin"[2][3]. The Echinoderms are important both biologically and geologically: biologically because few other groupings are so abundant in the biotic desert of the deep sea, as well as the shallower oceans, and geologically as their ossified skeletons are major contributors to many limestone formations, and can provide valuable clues as to the geological environment. Further, it is held by some that the radiation of echinoderms was responsible for the Mesozoic revolution of marine life. Two main subdivisions of Echinoderms are traditionally recognised: the more familiar, motile Eleutherozoa, which encompasses the Asteroidea (starfish), Ophiuroidea (brittle stars), Echinoidea (sea urchins and sand dollars) and Holothuroidea (sea cucumbers); and the sessile Pelmatazoa, which consists of the crinoids. Some crinoids, the feather stars, have secondarily re-evolved a free-living lifestyle. A fifth class of Eleutherozoa consisting of just two species, the Concentricycloidea (sea daisies), were recently[4] merged into the Asteroidea. The fossil record contains a host of other classes which do not appear to fall into any extant crown group.

Talks Juan Enriquez: Beyond the crisis, mindboggling science and the arrival of Homo evolutis (Skip to minute 7:50)

2009-03-02T21:11:00.002-05:00

He talks for about 7 minutes about finance. Most of us know all this already so skip to the good part! Go to minute 7:50. That's when he starts his most excellent recap of the latest BIO technology.

Developmental Biology of a Simple Organism by Richard Losick, April 2008 - Part 1: How Bacillus Subtilis Makes a Spore (28:57)

2009-03-02T15:17:00.002-05:00

How do simple cells differentiate, assemble into communities, and cope with change? Losick's seminar addresses these questions in the spore-forming bacterium Bacillus subtilis. Part I is an overview of how B. subtilis makes a spore. For further information see: http://www.ascb.org/ibioseminars/Losick/Losick1.cfm » More

How do simple cells differentiate, assemble into communities, and cope with change? Losick's seminar addresses these questions in the spore-forming bacterium Bacillus subtilis. Part I is an overview of how B. subtilis makes a spore.

Part 2: New Research on Multicellularity (18:13)

Part 3: Stochasticity and Cell Fate (25:03)

For further information see: http://www.ascb.org/ibioseminars/Losick/Losick1.cfm

Sex and Smell: Molecular Biology of Pheromone Perception by Catherine Dulac - Part 1: Introduction: Genes and Chemosensory Detection (15:31)

2009-03-02T10:39:00.003-05:00

Pheromones have evolved to signal the sex and the dominance status of animals and to promote social and mating rituals. In this lecture, I discuss the how pheromone sensing operates in mammals. I will discuss the molecular biology of the chemosensory receptors that are involved the first steps of pheromone sensing. At a higher level of complexity, I will discuss a distinct olfactory structure called the vomeronasal organ (VNO) and how it contributes to sex-specific behavioral responses.

For further information see: http://www.ascb.org/ibioseminars/Dulac/Dulac1.cfm

Part 2: Molecular Biology of Pheromone Perception (43:43)

Part 3: Sex-Specificity of Pheromone Responses (30:39)

dulac_powerpoint_pt1.pdf
Sex and Smell: Molecular Biology of Pheromone Perception (presentation slides)

We have discovered a new blog dedicated to LAB TUTORIALS!

2009-03-02T09:40:00.005-05:00

http://labtutorials.org/
Labtutorials in Biology is a blog that provides step-by-step tutorials in molecular biology. Bálint L. Bálint, junior lecturer, is behind the whole concept and he’s been making videos and writing descriptions for weeks.

For New Yorkers: NON BIO SPECIFIC - The Secret Science Club Lectures

2009-03-01T15:21:00.002-05:00

The Secret Science Club is a free science lecture and arts series. It is open to the public and meets the first Wednesday of every month in the basement of Union Hall in Park Slope, Brooklyn.

Find out more here: http://secretscienceclub.blogspot.com/

On Febuary 4th the club featured: Dr. Pieribone, A cellular and molecular biologist at Yale University’s School of Medicine and the co-author of Aglow in the Dark: The Revolutionary Science of Biofluorescence. Dr. Pieribone asked:
--What do jellyfish and coral reefs have to do with the human brain and quest for medical cures?
--What makes undersea animals glow?
--How can biofluorescent technology link the human mind with machines?
--What are the latest advances in fluorescent micro-photography?
--And whatever happened to that transgenic, glow-in-the-blacklight rabbit in France?

UC BERKLEY General Biochemistry and Molecular Biology

2009-03-01T03:33:00.002-05:00

Video Lecture Description	Sub-Category	Time	Click to view video
Lecture1-DNA Structure	Biochemistry	49m 32s	Click to view video lecture
Lecture2-Variation in DNA Structure and Recognition	Biochemistry	50m 30s	Click to view video lecture
Lecture3-Principles of RNA Structure	Biochemistry	50m 24s	Click to view video lecture
Lecture4-DNA Polymerases	Biochemistry	51m 06s	Click to view video lecture
Lecture5-The DNA Replication Fork	Biochemistry	48m 33s	Click to view video lecture
Lecture6-Other Replication Factors	Biochemistry	55m 56s	Click to view video lecture
Lecture7-Replication Origins and Ends	Biochemistry	53m 17s	Click to view video lecture
Lecture8-DNA Analysis Methods	Biochemistry	50m 03s	Click to view video lecture
Lecture9-Chromatin Structure and Dynamics	Biochemistry	48m 38s	Click to view video lecture
Lecture10-Genome Structure	Biochemistry	46m 49s	Click to view video lecture
Lecture11-Genomics and Bioinformatics	Biochemistry	51m 06s	Click to view video lecture
Lecture12-DNA Damage and Repair	Biochemistry	50m 57s	Click to view video lecture
Lecture13-DNA Damage and Repair in Cancer	Biochemistry	51m 04s	Click to view video lecture
Lecture14-Human Disease Genes	Biochemistry	49m 44s	Click to view video lecture
Lecture15-Prokaryotic Transcription Apparatus I	Biochemistry	44m 35s	Click to view video lecture
Lecture16-Prokaryotic Transcription Apparatus II	Biochemistry	50m 58s	Click to view video lecture
Lecture17-Control of Prokaryotic Transcription I	Biochemistry	49m 57s	Click to view video lecture
Lecture18-Control of Prokaryotic Transcription II	Biochemistry	47m 19s	Click to view video lecture
Lecture19-Eukaryotic Transcription Apparatus-Methods to Analyze Transcription I	Biochemistry	49m 25s	Click to view video lecture
Lecture20-Eukaryotic Transcription Apparatus-Methods to Analyze Transcription II	Biochemistry	49m 40s	Click to view video lecture
Lecture21-Eukaryotic Transcription Apparatus-Methods to Analyze Transcription III	Biochemistry	50m 10s	Click to view video lecture
Lecture22-Control of Eukaryotic Transcription I	Biochemistry	47m 18s	Click to view video lecture
Lecture23-Control of Eukaryotic Transcription II	Biochemistry	47m 07s	Click to view video lecture
Lecture24-Control of Eukaryotic Transcription III	Biochemistry	51m 14s	Click to view video lecture
Lecture25-RNA Processing I	Biochemistry	49m 39s	Click to view video lecture
Lecture26-RNA Processing II	Biochemistry	49m 20s	Click to view video lecture
Lecture27-Control of Translation I	Biochemistry	50m 25s	Click to view video lecture
Lecture28-Control of Translation II	Biochemistry	40m 39s	Click to view video lecture
Lecture29-Membrane Structure I	Biochemistry	52m 04s	Click to view video lecture
Lecture30-Membrane Structure II	Biochemistry	51m 01s	Click to view video lecture
Lecture31-Membrane Structure III and Transport of Small Molecules I	Biochemistry	38m 00s	Click to view video lecture
Lecture32-Transport of Small Molecules II	Biochemistry	49m 56s	Click to view video lecture
Lecture33-Assembly of Proteins in Membranes I	Biochemistry	48m 45s	Click to view video lecture
Lecture34-Assembly of Proteins in Membranes II	Biochemistry	50m 16s	Click to view video lecture
Lecture35-Transport Into and Out of Nucleus I	Biochemistry	48m 09s	Click to view video lecture
Lecture36-Transport Into and Out of Nucleus II-Intracellular Transport of Proteins I	Biochemistry	51m 05s	Click to view video lecture
Lecture37-Intracellular Transport of Proteins II	Biochemistry	49m 49s	Click to view video lecture
Lecture38-Intracellular Transport of Proteins III	Biochemistry	47m 48s	Click to view video lecture
Lecture39-Hormones and Signal Transduction I	Biochemistry	49m 03s	Click to view video lecture
Lecture40-Hormones and Signal Transduction II	Biochemistry	46m 59s	Click to view video lecture
Lecture41-Hormones and Signal Transduction III and Cell Division Cycle I	Biochemistry	47m 48s	Click to view video lecture
Lecture42-Cell Division Cycle II	Biochemistry	38m 32s	Click to view video lecture